def isosurfacePlot(self, stay=False, samples=100, contours=50):
visit.AddWindow()
returned = []
if len(visit.ListPlots()) > 0:
visit.SetActivePlots(0)
visit.HideActivePlots()
p = visit.PseudocolorAttributes()
q = visit.ResampleAttributes()
r = visit.IsosurfaceAttributes()
q.samplesX = samples
q.samplesY = samples
q.samplesZ = samples
r.contourNLevels = contours
plot = visit.AddPlot("Pseudocolor", "Heat")
visit.AddOperator("Resample")
# visit.AddOperator("Isosurface")
visit.SetOperatorOptions(q)
visit.SetOperatorOptions(r)
visit.SetPlotOptions(p)
visit.DrawPlots()
returned.append(visit.SaveWindow())
count = 0
visit.AddOperator("Isosurface")
visit.DrawPlots()
time.sleep(60)
returned.append(visit.SaveWindow())
return returned
def plane_slice_plotting(window_number, axis_number, label, images, timestamp):
"""
Copy the Mesh, Pseudocolor, and Contour plots into a new VisIt window and
slice through the proper axis.
Input:
______
window_number: int
The number of the window to open (2,3, or 4).
axis_number: int
The number of the axis to slice through (0 for X, 1 for Y, 2 for Z).
label: str
The title of the plane slice.
images: boolean
Whether or not to save images of the plot windows.
timestamp: boolean
Whether or not to keep the timestamp on plot window images.
Returns:
________
none
"""
# Open a new window with all three plots.
Vi.AddWindow()
Vi.CopyPlotsToWindow(1, window_number)
# Create the plane slice plot by activating the mesh, pseudocolor, and contour plots.
Vi.SetActiveWindow(window_number)
Vi.SetActivePlots((0, 1, 2))
# Remove the clip and slice operators from previous plot windows.
Vi.RemoveAllOperators()
# Add a slice through the proper axis.
Vi.AddOperator("Slice", 1)
s = Vi.SliceAttributes()
s.axisType = axis_number
Vi.SetOperatorOptions(s)
# Include a label for each plane slice plot.
banner = Vi.CreateAnnotationObject("Text2D")
banner.position = (0.45, 0.92)
banner.text = label
banner.height = 0.05
# Include the CNERG logo in the bottom left corner of the plot.
image = Vi.CreateAnnotationObject("Image")
image.image = os.path.dirname(os.path.abspath(__file__)) + "/cnerg.jpg"
image.position = (0.02, 0.02)
image.width = 10
image.height = 10
Vi.DrawPlots()
if images:
if timestamp:
attributes = Vi.GetAnnotationAttributes()
attributes.userInfoFlag = 0
Vi.SetAnnotationAttributes(attributes)
Vi.SaveWindow()
def createSnowPseudocolor(self,
varname,
limits=None,
cmap=None,
window=None,
legend=False):
"""Simplified interface to create standard pseudocolors on the snow surface."""
self.activateSurface()
if window is not None:
self.setActiveWindow(window)
win = self.getActiveWindow()
if cmap is None:
cmap = "hot"
pcolor = win.createPseudocolor(varname,
limits=limits,
cmap=cmap,
legend=legend)
# deform by surface vector
v.AddOperator("Displace")
da = v.DisplaceAttributes()
da.variable = "snow_displace"
v.SetOperatorOptions(da)
pcolor.operators.append(Operator("displace", "Displace", da))
return pcolor
def binPhase(eDB):
visit.OpenDatabase(eDB, 0)
visit.AddPlot("Pseudocolor", "operators/DataBinning/2D/electrons", 1, 1)
DataBinningAtts = visit.DataBinningAttributes()
DataBinningAtts.numDimensions = DataBinningAtts.Two # One, Two, Three
DataBinningAtts.dim1BinBasedOn = DataBinningAtts.Variable # X, Y, Z, Variable
DataBinningAtts.dim1Var = "electrons_zSI"
DataBinningAtts.dim1SpecifyRange = 1
DataBinningAtts.dim1MinRange = 0
DataBinningAtts.dim1MaxRange = 1.0E-7
DataBinningAtts.dim1NumBins = 100
DataBinningAtts.dim2BinBasedOn = DataBinningAtts.Variable # X, Y, Z, Variable
DataBinningAtts.dim2Var = "electrons_gamma"
DataBinningAtts.dim2SpecifyRange = 1
DataBinningAtts.dim2MinRange = 0.991
DataBinningAtts.dim2MaxRange = 1.005
DataBinningAtts.dim2NumBins = 100
DataBinningAtts.outOfBoundsBehavior = DataBinningAtts.Clamp # Clamp, Discard
DataBinningAtts.reductionOperator = DataBinningAtts.Sum # Average, Minimum, Maximum, StandardDeviation, Variance, Sum, Count, RMS, PDF
DataBinningAtts.varForReduction = "electrons_chargeSI"
DataBinningAtts.emptyVal = 0
DataBinningAtts.outputType = DataBinningAtts.OutputOnBins # OutputOnBins, OutputOnInputMesh
DataBinningAtts.removeEmptyValFromCurve = 1
visit.SetOperatorOptions(DataBinningAtts, 1)
visit.SetTimeSliderState(0)
visit.SetTimeSliderState(1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.centering = PseudocolorAtts.Nodal # Natural, Nodal, Zonal
PseudocolorAtts.opacityType = PseudocolorAtts.Ramp # ColorTable, FullyOpaque, Constant, Ramp, VariableRange
PseudocolorAtts.colorTableName = "hot_desaturated"
visit.SetPlotOptions(PseudocolorAtts)
View2DAtts = visit.View2DAttributes()
View2DAtts.fullFrameActivationMode = View2DAtts.On
# View2DAtts.fullFrameAutoThreshold = 100
visit.SetView2D(View2DAtts)
visit.ResetView()
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.axes2D.yAxis.grid = 0
AnnotationAtts.axes2D.xAxis.grid = 0
AnnotationAtts.axes2D.xAxis.title.userTitle = 1
AnnotationAtts.axes2D.xAxis.title.userUnits = 1
AnnotationAtts.axes2D.xAxis.title.title = "ct-z"
AnnotationAtts.axes2D.xAxis.title.units = "m"
AnnotationAtts.axes2D.yAxis.title.userTitle = 1
AnnotationAtts.axes2D.yAxis.title.userUnits = 1
AnnotationAtts.axes2D.yAxis.title.title = "gamma"
AnnotationAtts.axes2D.yAxis.title.units = ""
AnnotationAtts.userInfoFlag = 0
AnnotationAtts.databaseInfoFlag = 0
# AnnotationAtts.legendInfoFlag = 0
visit.SetAnnotationAttributes(AnnotationAtts)
visit.DrawPlots()
def test_query_02_kwargs(self):
#add a threshold
visit.AddOperator("Isovolume")
iatts = visit.IsovolumeAttributes()
iatts.lbound = 0.4
iatts.ubound = 1e+37
visit.SetOperatorOptions(iatts)
visit.DrawPlots()
res_v = query("Min", use_actual_data=True)
self.assertTrue(abs(res_v - 0.3778594434261322) < 1e-5)
res_v = query("Min", use_actual_data=False)
self.assertTrue(abs(res_v - 0.02357020415365696) < 1e-5)
def __get_isovol(self, lbound, ubound, i):
"""Gets the volume selection for isovolume and export just the
outer surface of the volume as STL.
Input:
------
lbound: float, lower boundary value for the isovolume
ubound: float, upper boundary value for the isovolume
i: int, surface number
"""
# generate isovolume
v.AddOperator("Isovolume")
att = v.IsovolumeAttributes()
att.lbound = lbound
att.ubound = ubound
v.SetOperatorOptions(att)
# set operator setting to only get surfaces meshes
v.AddOperator("ExternalSurface")
# draw plot
v.DrawPlots()
# export current volume to folder
e = v.ExportDBAttributes()
e.dirname = self.db + "/vols/"
e.db_type = "STL"
e.filename = str(i)
e.variables = self.data
export_res = v.ExportDatabase(e)
# check if exporting was successful or not and adjust values
if export_res == 0:
# export not successful because there was no data
# get new upper bound
warn_message = "Warning: no data to export between " \
+ "{} and {}.\n".format(lbound, ubound) \
+ "Increasing upper bound to next selected level."
warnings.warn(warn_message)
if ubound == max(self.levels):
# already at max so do not need to export more levels
self.levels.remove(ubound)
export_res = 1
else:
# update to next level to try again
index = self.levels.index(ubound)
ubound_old = ubound
ubound = self.levels[index + 1]
self.levels.remove(ubound_old)
# delete the operators
v.RemoveAllOperators()
return export_res, ubound
def _get_isovol(self, lbound, ubound, i):
"""Gets the volume selection for isovolume and export just the
outer surface of the volume as STL.
Input:
------
lbound: float, lower boundary value for the isovolume
ubound: float, upper boundary value for the isovolume
i: int, surface number
"""
# generate isovolume
v.AddOperator("Isovolume")
att = v.IsovolumeAttributes()
att.lbound = lbound
att.ubound = ubound
v.SetOperatorOptions(att)
# set operator setting to only get surfaces meshes
v.AddOperator("ExternalSurface")
# draw plot
draw_res = v.DrawPlots()
if draw_res == 0:
sys.exit("Error with producing isovolume")
# export current volume to folder
e = v.ExportDBAttributes()
e.dirname = self.db + "/vols/"
e.db_type = "STL"
e.filename = str(i)
e.variables = self.data
export_res = v.ExportDatabase(e)
if export_res == 0:
# export not successful because there was no data
# get new upper bound
warn_message = "Warning: no data to export between {} and {}.\n".format(lbound, ubound) \
+ "Increasing upper bound to next selected level."
print(warn_message)
if ubound in self.levels:
self._update_levels(ubound)
else:
# it is the arbitrary upper level set and is not needed
self._update_levels(self.levels[-1])
# delete the operators
v.RemoveAllOperators()
return export_res, ubound
def draw(self):
print "drawing window %d of dimension %d"%(self.i,self.dim)
v.SetActiveWindow(self.i)
v.SetAnnotationAttributes(self.annot)
if self.dim == 2:
# add the slice
assert self._slice is not None
for i,plot in enumerate(self.plots):
sliced = False
for op in plot.operators:
if "slice" == op.oname:
sliced = True
if not sliced:
print "slicing plot %d..."%i
v.SetActivePlots(i)
v.AddOperator("Slice")
sa = self._slice.toAttributes()
v.SetOperatorOptions(sa)
plot.operators.append(Operator("slice", "Slice", sa))
if self.exaggeration is not None:
print "exaggerating..."
self._exaggerateVertical()
# set the plot options
for i, plot in enumerate(self.plots):
print "setting plot options for plot %i..."%i
v.SetActivePlots(i)
v.SetPlotOptions(plot.patts)
# set the view
print "setting the view..."
if self.dim == 2:
v.SetView2D(self.view)
else:
v.SetView3D(self.view)
print "drawing..."
v.DrawPlots()
def _exaggerateVertical(self):
if self.dim == 3:
self.view.axis3DScaleFlag = 1
self.view.axis3DScales = (self.view.axis3DScales[0],
self.view.axis3DScales[1],
self.exaggeration)
else:
for i,plot in enumerate(self.plots):
done = False
for op in plot.operators:
if "exaggerate_vertical" == op.oname:
done = True
if not done:
print "transforming plot %d..."%i
tr = v.TransformAttributes()
tr.doScale = 1
tr.scaleY = self.exaggeration
v.SetActivePlots(i)
v.AddOperator("Transform")
v.SetOperatorOptions(tr)
plot.operators.append(Operator("exaggerate_vertical", "Transform", tr))
def surfIntens(fDB):
visit.OpenDatabase(fDB, 0)
visit.AddPlot("Pseudocolor", "operators/DataBinning/2D/meshScaled", 1, 1)
DataBinningAtts = visit.DataBinningAttributes()
DataBinningAtts.numDimensions = DataBinningAtts.Two # One, Two, Three
DataBinningAtts.dim1BinBasedOn = DataBinningAtts.X # X, Y, Z, Variable
DataBinningAtts.dim1Var = "default"
DataBinningAtts.dim1SpecifyRange = 0
DataBinningAtts.dim1MinRange = 0
DataBinningAtts.dim1MaxRange = 1
DataBinningAtts.dim1NumBins = 85
DataBinningAtts.dim2BinBasedOn = DataBinningAtts.Y # X, Y, Z, Variable
DataBinningAtts.dim2Var = "default"
DataBinningAtts.dim2SpecifyRange = 0
DataBinningAtts.dim2MinRange = 0
DataBinningAtts.dim2MaxRange = 1
DataBinningAtts.dim2NumBins = 85
DataBinningAtts.dim3BinBasedOn = DataBinningAtts.Variable # X, Y, Z, Variable
DataBinningAtts.dim3Var = "default"
DataBinningAtts.dim3SpecifyRange = 0
DataBinningAtts.dim3MinRange = 0
DataBinningAtts.dim3MaxRange = 1
DataBinningAtts.dim3NumBins = 50
DataBinningAtts.outOfBoundsBehavior = DataBinningAtts.Clamp # Clamp, Discard
DataBinningAtts.reductionOperator = DataBinningAtts.Average # Average, Minimum, Maximum, StandardDeviation, Variance, Sum, Count, RMS, PDF
DataBinningAtts.varForReduction = "intensityScaled"
DataBinningAtts.emptyVal = 0
DataBinningAtts.outputType = DataBinningAtts.OutputOnBins # OutputOnBins, OutputOnInputMesh
DataBinningAtts.removeEmptyValFromCurve = 1
visit.SetOperatorOptions(DataBinningAtts, 1)
View2DAtts = visit.View2DAttributes()
View2DAtts.fullFrameActivationMode = View2DAtts.On
# View2DAtts.fullFrameAutoThreshold = 100
visit.SetView2D(View2DAtts)
visit.ResetView()
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.centering = PseudocolorAtts.Nodal # Natural, Nodal, Zonal
visit.SetPlotOptions(PseudocolorAtts)
visit.DrawPlots()
def make_distribution_movie(cellids,
rotated,
inputDirectory,
outputDirectory,
outputFileName,
zoom=1.0,
viewNormal=[0.488281, 0.382966, -0.784167],
minThreshold=1e-18,
maxThreshold=1e37):
'''Makes a distribution movie of some given distribution data
Example usage:
make_distribution_movie(cellids=[18302, 19432, 19042], rotated=True, inputDirectory=\"/home/hannukse/meteo/stornext/field/vlasiator/2D/AAJ/silo_files/\", outputDirectory=\"/home/hannukse/MOVIES/\", outputFileName=\"testmovie\", zoom=0.8, viewNormal=[0.488281, 0.382966, -0.784167], minThreshold=1e-17, maxThreshold=1.2e37)
Note: viewNormal determines the angle of view (straight from visit)
'''
if len(viewNormal) != 3:
print "ERROR, INVALID VIEWNORMAL LENGTH, SHOULD BE 3"
return
for cell in sorted(cellids):
# OPTIONS
###########################################################
cellid = str(cell)
#databaseName = "localhost:/home/hannukse/meteo/lustre/tmp/hannuksela/AAM/velgrid.rotated." + cellid + ".*.silo database"
if rotated == True:
rotateFix = "rotated."
else:
rotateFix = ""
inputFileName = "velgrid." + rotateFix + cellid + ".*.silo"
databaseName = "localhost:" + inputDirectory + inputFileName + " database"
outputDir = outputDirectory
fileName = outputFileName + "_" + cellid + "_"
WIDTH = 3000
HEIGHT = 3000
# Threshold values:
# TODO: USE VLSV READER TO AUTOMATE THIS
minimumThreshold = minThreshold
maximumThreshold = maxThreshold
###########################################################
vis.OpenDatabase(databaseName, 0)
#Load settings
visSettings.load_visit_settings()
#Make a plot
vis.AddPlot("Pseudocolor", "avgs", 1, 1)
vis.SetActivePlots(0)
vis.AddOperator("Threshold", 1)
vis.ThresholdAtts = vis.ThresholdAttributes()
vis.ThresholdAtts.outputMeshType = 0
vis.ThresholdAtts.listedVarNames = ("default")
vis.ThresholdAtts.zonePortions = (1)
vis.ThresholdAtts.lowerBounds = (minimumThreshold)
vis.ThresholdAtts.upperBounds = (maximumThreshold)
vis.ThresholdAtts.defaultVarName = "avgs"
vis.ThresholdAtts.defaultVarIsScalar = 1
vis.SetOperatorOptions(vis.ThresholdAtts, 1)
vis.DrawPlots()
# Begin spontaneous state
vis.View3DAtts = vis.View3DAttributes()
vis.View3DAtts.viewNormal = (viewNormal[0], viewNormal[1],
viewNormal[2])
vis.View3DAtts.focus = (-634.56, 91.3781, -13.7891)
vis.View3DAtts.viewUp = (-0.102795, 0.917551, 0.3841)
vis.View3DAtts.viewAngle = 30
vis.View3DAtts.parallelScale = 1.45614e+06
vis.View3DAtts.nearPlane = -2.91228e+06
vis.View3DAtts.farPlane = 2.91228e+06
vis.View3DAtts.imagePan = (0, 0)
vis.View3DAtts.imageZoom = zoom
vis.View3DAtts.perspective = 1
vis.View3DAtts.eyeAngle = 2
vis.View3DAtts.centerOfRotationSet = 0
vis.View3DAtts.centerOfRotation = (-634.56, 91.3781, -13.7891)
vis.View3DAtts.axis3DScaleFlag = 0
vis.View3DAtts.axis3DScales = (1, 1, 1)
vis.View3DAtts.shear = (0, 0, 1)
vis.SetView3D(vis.View3DAtts)
# End spontaneous state
vis.ViewCurveAtts = vis.ViewCurveAttributes()
vis.ViewCurveAtts.domainCoords = (0, 1)
vis.ViewCurveAtts.rangeCoords = (0, 1)
vis.ViewCurveAtts.viewportCoords = (0.2, 0.95, 0.15, 0.95)
vis.ViewCurveAtts.domainScale = vis.ViewCurveAtts.LINEAR # LINEAR, LOG
vis.ViewCurveAtts.rangeScale = vis.ViewCurveAtts.LINEAR # LINEAR, LOG
vis.SetViewCurve(vis.ViewCurveAtts)
vis.View2DAtts = vis.View2DAttributes()
vis.View2DAtts.windowCoords = (0, 1, 0, 1)
vis.View2DAtts.viewportCoords = (0.2, 0.95, 0.15, 0.95)
vis.View2DAtts.fullFrameActivationMode = vis.View2DAtts.Auto # On, Off, Auto
vis.View2DAtts.fullFrameAutoThreshold = 100
vis.View2DAtts.xScale = vis.View2DAtts.LINEAR # LINEAR, LOG
vis.View2DAtts.yScale = vis.View2DAtts.LINEAR # LINEAR, LOG
vis.View2DAtts.windowValid = 0
vis.SetView2D(vis.View2DAtts)
vis.View3DAtts = vis.View3DAttributes()
vis.View3DAtts.viewNormal = (viewNormal[0], viewNormal[1],
viewNormal[2])
vis.View3DAtts.focus = (-634.56, 91.3781, -13.7891)
vis.View3DAtts.viewUp = (-0.102795, 0.917551, 0.3841)
vis.View3DAtts.viewAngle = 30
vis.View3DAtts.parallelScale = 1.45614e+06
vis.View3DAtts.nearPlane = -2.91228e+06
vis.View3DAtts.farPlane = 2.91228e+06
vis.View3DAtts.imagePan = (0, 0)
vis.View3DAtts.imageZoom = zoom
vis.View3DAtts.perspective = 1
vis.View3DAtts.eyeAngle = 2
vis.View3DAtts.centerOfRotationSet = 0
vis.View3DAtts.centerOfRotation = (-634.56, 91.3781, -13.7891)
vis.View3DAtts.axis3DScaleFlag = 0
vis.View3DAtts.axis3DScales = (1, 1, 1)
vis.View3DAtts.shear = (0, 0, 1)
vis.SetView3D(vis.View3DAtts)
vis.ViewAxisArrayAtts = vis.ViewAxisArrayAttributes()
vis.ViewAxisArrayAtts.domainCoords = (0, 1)
vis.ViewAxisArrayAtts.rangeCoords = (0, 1)
vis.ViewAxisArrayAtts.viewportCoords = (0.15, 0.9, 0.1, 0.85)
vis.SetViewAxisArray(vis.ViewAxisArrayAtts)
for i in range(0, vis.GetDatabaseNStates()):
vis.SetTimeSliderState(i)
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = outputDir
vis.SaveWindowAtts.fileName = fileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = WIDTH
vis.SaveWindowAtts.height = HEIGHT
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
# Make the movie:
framerate = 5
subprocess.call([
pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh",
outputDir, fileName, framerate
])
def _updateDisplay(self,bSameDomain):
print("")
print("_updateDisplay() - start ..... variable="+str(self._variable)+", plot="+str(self._currentPlot)+", op="+str(self._currentOperator)+", opEnabled="+str(self._operatorEnabled))
#
# remove old plot if not applicable
#
if (bSameDomain == False or (self._currentPlot != None and (self._variable == None or (self._currentPlot[1] != self._variable)))):
print(" _updateDisplay() - removing plots and operators")
visit.DeleteAllPlots()
self._currentPlot = None
visit.RemoveAllOperators()
self._currentOperator = None
#
# remove old operator if not needed
#
if (self._currentOperator != None and self._operatorEnabled == False):
print(" _updateDisplay() - removing operators, operatorEnabled is False")
visit.RemoveAllOperators()
self._currentOperator = None
#
# remove old operator if wrong type
#
if (self._currentOperator == "Slice" and self._operatorProject2d == False):
print(" _updateDisplay() - removing operators, 'Slice' incompatible with project2d==False")
visit.RemoveAllOperators()
self._currentOperator = None
if (self._currentOperator == "Clip" and self._operatorProject2d == True):
print(" _updateDisplay() - removing operators, 'Clip' incompatible with project2d==True")
visit.RemoveAllOperators()
self._currentOperator = None
#
# add new plot if needed
#
if (self._variable != None and self._currentPlot == None):
print(" _updateDisplay() - adding 'Pseudocolor' plot for variable '"+str(self._variable)+"'")
print(" _updateDisplay() -- variable without str = ")
print(self._variable)
visit.AddPlot("Pseudocolor", str(self._variable))
visit.SetPlotOptions(self._pseudocolorAttributes)
self._currentPlot = ("Pseudocolor",str(self._variable))
# Turn off display database name in plot window to reduce clutter
attributes = visit.AnnotationAttributes()
attributes.databaseInfoFlag=0
visit.SetAnnotationAttributes(attributes)
#
# if operator needed, set operator attributes (add new operator if needed)
#
if (self._operatorEnabled == True and self._currentPlot != None):
#
# if no operator, then add one
#
if (self._currentOperator == None):
if (self._operatorProject2d):
print(" _updateDisplay() - adding operator 'Slice'")
visit.AddOperator("Slice")
self._currentOperator = "Slice"
else:
print(" _updateDisplay() - adding operator 'Clip'")
visit.AddOperator("Clip")
self._currentOperator = "Clip"
#
# set operator attributes
#
if (self._currentOperator == "Slice"):
print(" _updateDisplay() - setting operator options for 'Slice'")
visit.SetOperatorOptions(self._getSliceAttributes())
else:
print(" _updateDisplay() - setting operator options for 'Clip'")
visit.SetOperatorOptions(self._getClipAttributes())
#
# Redraw
#
print(" _updateDisplay() - redrawing")
visit.DrawPlots()
print("_updateDisplay() - end")
print("")
# First fig
for alpha in (0.05, 0.6):
visit.AddPlot("Pseudocolor", "vol_frac_average", 1, 1)
visit.AddOperator("Slice", 1)
SliceAtts = visit.SliceAttributes()
SliceAtts.originType = SliceAtts.Point
SliceAtts.originPoint = (0, 0, 0)
SliceAtts.normal = (0, 0, -1)
SliceAtts.axisType = SliceAtts.ZAxis
SliceAtts.upAxis = (1, 0, 0)
SliceAtts.project2d = 1
SliceAtts.flip = 1
visit.SetOperatorOptions(SliceAtts, 1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag = 1
PseudocolorAtts.min = 0.
PseudocolorAtts.maxFlag = 1
PseudocolorAtts.max = alpha
visit.SetPlotOptions(PseudocolorAtts)
View2DAtts = visit.View2DAttributes()
View2DAtts.windowCoords = (-0.01, 0.07, 0, 1.58)
View2DAtts.viewportCoords = (0.7, 0.95, 0.1, 0.95)
visit.SetView2D(View2DAtts)
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.axes2D.autoSetTicks = 0
def make_movie( variableName, minValue, maxValue, inputDirectory, inputFileName, outputDirectory, outputFileName, colorTable="hot_desaturated", startFrame=-1, endFrame=-1 ):
'''
Function for making a movie
Arguments:
:param variableName Name of the variable
:param minValue Minimum value of the variable
:param maxValue Maximum value of the variable
:param inputDirectory Path to input vlsv/silo files
:param inputFileName Name of the file(s) so for example if the filenames are bulk.0000.silo, bulk.0001.silo, .. then inputFileName=\"bulk.*.silo\""
:param outputDirectory Path to output directory
:param outputFileName Name of the output file
:param colorTable="hot_desaturated" Color table for the plots
:param startFrame=-1 Starting frame of the movie (-1 equals 0)
:param endFrame=-1 Starting frame of the movie (-1 equals last frame)
'''
# OPTIONS
#################################################################
# Input frame properties
_startFrame = startFrame # Note: if _startFrame is set to -1 the start frame gets set to 0
_endFrame = endFrame # Note: if _endFrame is set to -1 the _endFrame is automatically the number of frames in the database
# Input variable
_variableName = variableName
minVariableValue = minValue
maxVariableValue = maxValue
colorTableName = colorTable
# Input directory and file names
#_outputDir = "/home/hannukse/MOVINGFRAME_MOVIES/AAJ_BZ_REMAKE/" # Set the output directory (Where .png s are saved)
_outputDir = outputDirectory
#_outputFileName = "BZ_FORESHOCK_2_" # The file names for the png files. These for ex. will be saved visit0000.png, visit0001.png, ..
_outputFileName = outputFileName # The file names for the png files.
#databaseName = "localhost:/home/hannukse/meteo/stornext/field/vlasiator/2D/AAJ/silo_files/bulk.*.silo database" # For navigating to the silo files
databaseName = "localhost:" + inputDirectory + inputFileName + " database" # For navigating to the silo files
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
# LaunchNowin(vdir=visitBinDirectory)
#dx = speedX * frameInSeconds # Note: This is in meters per frame!
#dy = speedY * frameInSeconds # Note: This is in meters per frame!
#LaunchNowin(vdir="/usr/local/visit/bin")
#Set up window and annotations
#vis.LaunchNowin(vdir="/usr/local/visit/bin")
vis.OpenDatabase(databaseName, 0)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Pseudocolor", _variableName, 1, 1) #CONTINUE
vis.SetActivePlots(0)
vis.PseudocolorAtts = vis.PseudocolorAttributes()
vis.PseudocolorAtts.legendFlag = 1
vis.PseudocolorAtts.lightingFlag = 1
vis.PseudocolorAtts.minFlag = 1
vis.PseudocolorAtts.maxFlag = 1
vis.PseudocolorAtts.centering = vis.PseudocolorAtts.Natural # Natural, Nodal, Zonal
vis.PseudocolorAtts.scaling = vis.PseudocolorAtts.Linear # Linear, Log, Skew
vis.PseudocolorAtts.limitsMode = vis.PseudocolorAtts.CurrentPlot # OriginalData, CurrentPlot
vis.PseudocolorAtts.min = minVariableValue
vis.PseudocolorAtts.max = maxVariableValue
vis.PseudocolorAtts.pointSize = 0.05
vis.PseudocolorAtts.pointType = vis.PseudocolorAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.PseudocolorAtts.skewFactor = 1
vis.PseudocolorAtts.opacity = 1
vis.PseudocolorAtts.colorTableName = colorTableName
vis.PseudocolorAtts.invertColorTable = 0
vis.PseudocolorAtts.smoothingLevel = 0
vis.PseudocolorAtts.pointSizeVarEnabled = 0
vis.PseudocolorAtts.pointSizeVar = "default"
vis.PseudocolorAtts.pointSizePixels = 2
vis.PseudocolorAtts.lineStyle = vis.PseudocolorAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.PseudocolorAtts.lineWidth = 0
vis.PseudocolorAtts.opacityType = vis.PseudocolorAtts.Explicit # Explicit, ColorTable
vis.SetPlotOptions(vis.PseudocolorAtts)
vis.SetActivePlots(0)
vis.AddOperator("Slice", 1)
vis.SetActivePlots(0)
vis.SliceAtts = vis.SliceAttributes()
vis.SliceAtts.originType = vis.SliceAtts.Intercept # Point, Intercept, Percent, Zone, Node
vis.SliceAtts.originPoint = (0, 0, 0)
vis.SliceAtts.originIntercept = 0
vis.SliceAtts.originPercent = 0
vis.SliceAtts.originZone = 0
vis.SliceAtts.originNode = 0
vis.SliceAtts.normal = (0, 0, 1)
vis.SliceAtts.axisType = vis.SliceAtts.ZAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
vis.SliceAtts.upAxis = (0, 1, 0)
vis.SliceAtts.project2d = 1
vis.SliceAtts.interactive = 1
vis.SliceAtts.flip = 0
vis.SliceAtts.originZoneDomain = 0
vis.SliceAtts.originNodeDomain = 0
vis.SliceAtts.meshName = "SpatialGrid"
vis.SliceAtts.theta = 0
vis.SliceAtts.phi = 90
vis.SetOperatorOptions(vis.SliceAtts, 1)
vis.DrawPlots()
if _endFrame == -1:
_endFrame = vis.TimeSliderGetNStates() - 1
if _startFrame == -1:
_startFrame = 0
# Iterate through frames
for i in range(_startFrame, _endFrame+1):
vis.SetTimeSliderState(i)
frame = i - _startFrame
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = _outputDir
vis.SaveWindowAtts.fileName = _outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = 3000
vis.SaveWindowAtts.height = 3000
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
# Make the movie:
#subprocess.call("./moviecompilescript.sh " + _outputDir + " " + _outputFileName)
pyVisitPath = "pyVisit/"
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh")
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh " + _outputDir + " " + _outputFileName)
framerate = "10"
subprocess.call([pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh", _outputDir, _outputFileName, framerate])
cc.perspective = 0
v.SetView3D(cc)
# Set box selection
if args.bbox:
v.AddOperator('Box')
batts = v.BoxAttributes()
batts.amount = batts.All # Some, All
batts.minx = args.bbox[0]
batts.maxx = args.bbox[1]
batts.miny = args.bbox[2]
batts.maxy = args.bbox[3]
batts.minz = args.bbox[4]
batts.maxz = args.bbox[5]
batts.inverse = 0
v.SetOperatorOptions(batts)
v.DrawPlots()
# Set output options
s = v.SaveWindowAttributes()
if args.fmt == 'png':
s.format = s.PNG
elif args.r == 'bmp':
s.format = s.BMP
elif args.r == 'jpg':
s.format = s.JPEG
s.width = args.width
s.height = args.height
s.screenCapture = 0
s.fileName = args.fname
def visit_plot_qcrit_wx_3d(xdmf_path,
qcrit_vals=(6.0, 1.0),
wx_lims=(-5.0, 5.0),
config_view=None,
out_dir=os.getcwd(),
prefix='qcrit_wx_3d_',
figsize=(1024, 1024),
state=None,
states=None,
states_range=[0, None, 1]):
"""Plot the 3D isosurface of the Q-criterion at 2 values.
The first isosurface is colored by the streamwise vorticity.
The second isosurface is colored with a single color (grey).
Parameters
----------
xdmf_path : str
Path of the XDMF file with information about the Q-criterion and
the streamwise vorticity.
qcrit_vals : tuple, optional
Values of the Q-criterion to display as a tuple of 2 floats;
default is (6.0, 1.0).
wx_lims : tuple, optional
Limits of the color range for the streamwise vorticity
as a tuple of 2 floats; default is (-5.0, 5.0).
config_view : str, optional
Path of the YAML file with the configuration of the view;
default is None (use default VisIt view).
out_dir : str, optional
Output directory in which figures will be saved;
default is the present working directory.
prefix : str, optional
Output filename prefix; default is "qcrit_wx_3d_".
figsize : tuple
Figure width and height (in pixels); default is (1024, 1024).
state : int, optional
Single state index to render;
default is None (i.e., render multiple states).
states : list, optional
List of states to render; default is None (i.e., render all states).
states_range : list, optional
Start, end, and step indices for states to render;
default is [0, None, 1] (i.e., render all states).
"""
visit_initialize()
# Open database from XDMF file.
visit.OpenDatabase(xdmf_path, 0)
# Add a pseudocolor of the streamwise vorticity.
visit.AddPlot('Pseudocolor', 'wx_cc', 1, 0)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag, PseudocolorAtts.maxFlag = 1, 1
PseudocolorAtts.min, PseudocolorAtts.max = wx_lims
PseudocolorAtts.colorTableName = 'viridis'
PseudocolorAtts.invertColorTable = 0
visit.SetPlotOptions(PseudocolorAtts)
# Add isosurface of the Q-criterion (colored by streamwise vorticity).
visit.AddOperator('Isosurface', 0)
IsosurfaceAtts = visit.IsosurfaceAttributes()
IsosurfaceAtts.contourMethod = IsosurfaceAtts.Value
IsosurfaceAtts.contourValue = (qcrit_vals[0])
IsosurfaceAtts.variable = 'qcrit'
visit.SetOperatorOptions(IsosurfaceAtts, 0)
# Add single-value contour of the Q-criterion.
visit.AddPlot('Contour', 'qcrit', 1, 0)
ContourAtts = visit.ContourAttributes()
ContourAtts.colorType = ContourAtts.ColorBySingleColor
ContourAtts.legendFlag = 0
ContourAtts.singleColor = (128, 128, 128, 153) # grey
ContourAtts.contourNLevels = 1
ContourAtts.minFlag, ContourAtts.maxFlag = 1, 1
ContourAtts.min, ContourAtts.max = qcrit_vals[1], qcrit_vals[1]
visit.SetPlotOptions(ContourAtts)
# Remove some annotations; keep triad.
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.userInfoFlag = 0
AnnotationAtts.databaseInfoFlag = 0
AnnotationAtts.timeInfoFlag = 0
AnnotationAtts.legendInfoFlag = 0
AnnotationAtts.axes3D.visible = 0
AnnotationAtts.axes3D.triadFlag = 1
AnnotationAtts.axes3D.bboxFlag = 0
visit.SetAnnotationAttributes(AnnotationAtts)
# Define state indices to render.
states = visit_get_states(state=state,
states=states,
states_range=states_range)
# Render states and save figures to files.
visit_render_save_states(states,
config_view=config_view,
out_dir=out_dir,
prefix=prefix,
figsize=figsize)
visit_finalize()
def visit_plot_qcrit_wx_3d(xdmf_dir,
wx_range=(-5.0, 5.0),
q_value=0.1,
config_view=None,
out_dir=os.getcwd(),
out_prefix='qcrit_wx_',
figsize=(1024, 1024),
state=None,
states=None,
states_range=[0, None, 1]):
visit_initialize()
# Define some variables to get the q_crit and wx_cc.
p_xdmf_path = os.path.join(str(xdmf_dir), 'p.xmf')
visit.OpenDatabase(p_xdmf_path, 0)
# Define cell-centered velocity vector field.
ux_xdmf_path = os.path.join(str(xdmf_dir), 'u.xmf')
uy_xdmf_path = os.path.join(str(xdmf_dir), 'v.xmf')
uz_xdmf_path = os.path.join(str(xdmf_dir), 'w.xmf')
vel_expr = ('{' +
'pos_cmfe(<{}[0]id:u>, <p Grid>, 1.0),'.format(ux_xdmf_path) +
'pos_cmfe(<{}[0]id:v>, <p Grid>, 0.0),'.format(uy_xdmf_path) +
'pos_cmfe(<{}[0]id:w>, <p Grid>, 0.0)'.format(uz_xdmf_path) +
'}')
visit.DefineVectorExpression('velocity', vel_expr)
# Define Q-criterion.
qcrit_expr = ('q_criterion(' + 'gradient(velocity[0]),' +
'gradient(velocity[1]),' + 'gradient(velocity[2])' + ')')
visit.DefineScalarExpression('q_crit', qcrit_expr)
# Define cell-centered streamwise vorticity.
wx_xdmf_path = os.path.join(str(xdmf_dir), 'wx.xmf')
wx_exp = 'pos_cmfe(<{}[0]id:wx>, <p Grid>, 0.0)'.format(wx_xdmf_path)
visit.DefineScalarExpression('wx_cc', wx_exp)
# Add a pseudocolor of the cell-centered streamwise vorticity.
visit.AddPlot('Pseudocolor', 'wx_cc', 1, 1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag = 1
PseudocolorAtts.min = wx_range[0]
PseudocolorAtts.maxFlag = 1
PseudocolorAtts.max = wx_range[1]
PseudocolorAtts.colorTableName = 'viridis'
PseudocolorAtts.invertColorTable = 0
PseudocolorAtts.opacityType = PseudocolorAtts.Constant
PseudocolorAtts.opacity = 0.8
PseudocolorAtts.legendFlag = 0
visit.SetPlotOptions(PseudocolorAtts)
# Add an isosurface of the Q-criterion.
visit.AddOperator('Isosurface', 1)
IsosurfaceAtts = visit.IsosurfaceAttributes()
IsosurfaceAtts.variable = 'q_crit'
IsosurfaceAtts.contourMethod = IsosurfaceAtts.Value
IsosurfaceAtts.contourValue = (q_value)
IsosurfaceAtts.scaling = IsosurfaceAtts.Linear
visit.SetOperatorOptions(IsosurfaceAtts, 1)
# Remove info about user, time, database, and legend.
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.userInfoFlag = 0
AnnotationAtts.databaseInfoFlag = 0
AnnotationAtts.timeInfoFlag = 0
AnnotationAtts.legendInfoFlag = 0
AnnotationAtts.axes3D.visible = 0
AnnotationAtts.axes3D.triadFlag = 1
AnnotationAtts.axes3D.bboxFlag = 0
visit.SetAnnotationAttributes(AnnotationAtts)
# Parse the 3D view configuration file.
if config_view is not None:
View3DAtts = visit_get_view(config_view, '3D')
visit.SetView3D(View3DAtts)
visit.SetActiveWindow(1)
states = visit_get_states(state=state,
states=states,
states_range=states_range)
visit_render_save_states(states,
out_dir=out_dir,
out_prefix=out_prefix,
figsize=figsize)
visit_finalize()
return
def make_moving_frame_of_reference_movie(x_begin,
x_end,
y_begin,
y_end,
speed_x,
speed_y,
variable_name,
minThreshold,
maxThreshold,
input_directory,
input_file_name,
output_directory,
output_file_name,
color_table="hot_desaturated",
start_frame=-1,
end_frame=-1,
frame_skip_dt=1.0):
'''
Function for making a movie with a moving frame of reference.
:param x_begin The starting frame's beginning x-coordinate
:param x_end The starting frame's ending x-coordinate
:param y_begin The starting frame's beginning x-coordinate
:param y_end The starting frame's ending y-coordinate
:param speed_x The speed at which the frame moves in the x direction
:param speed_y The speed at which the frame moves in the y direction
:param variable_name Name of the variable (For ex \"rho\")
:param minThreshold Minimum threshold for the variable
:param maxThreshold Maximum threshold for the variable
:param input_directory The path to the directory where the files are
:param input_file_name Name of the files (For ex \"bulk.*.silo\")
:param output_directory Directory where to output the movie
:param output_file_name Name of the outputted file (For ex \"RHOMOVIE\")
:param color_table Name of the color table (\"hot_desaturated\" by default)
:param start_frame Starting frame for the movie (if -1, equals 0, -1 by default)
:param end_frame Ending frame for the movie (if -1, equals the last frame, -1 by default)
:param frame_skip_dt The number of seconds one skip in frame equals (1.0 by default) (Note: This may change depending on the run and should always be checked)
'''
# OPTIONS
#################################################################
# Input the boundary box for starting coordinates (Starting values)
startX = x_begin # The left x-boundary of the box
endX = x_end # The right x-boundary of the box
startY = y_begin # The bottom y-boundary of the box
endY = y_end # The upper y-boundary of the box
# Input frame properties
startFrame = start_frame # Note: if startFrame is set to -1 the start frame gets set to 0
endFrame = end_frame # Note: if endFrame is set to -1 the endFrame is automatically the number of frames in the database
frameInSeconds = frame_skip_dt # Set how many seconds one frame skip is
# Input speed in x and y direction
speedX = speed_x # Meters per second
speedY = speed_y # Meters per second
# Input variable
variableName = variable_name
minVariableValue = minThreshold
maxVariableValue = maxThreshold
colorTableName = color_table
# Input directory and file names
outputDir = output_directory # Set the output directory (Where .png s are saved)
outputFileName = output_file_name # The file names for the png files. These for ex. will be saved visit0000.png, visit0001.png, .
databaseName = "localhost:" + input_directory + input_file_name + " database" # For navigating to the silo files
# visitBinDirectory = "/usr/local/visit/bin" #Nevermind this
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
# Launch visit
visitBinDirectory = '/home/htest/visit/bin'
vis.LaunchNowin(vdir=visitBinDirectory)
dx = speedX * frameInSeconds # Note: This is in meters per frame!
dy = speedY * frameInSeconds # Note: This is in meters per frame!
#Set up window and annotations
vis.OpenDatabase(databaseName, 0)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Pseudocolor", variableName, 1, 1)
vis.SetActivePlots(0)
vis.PseudocolorAtts = vis.PseudocolorAttributes()
vis.PseudocolorAtts.legendFlag = 1
vis.PseudocolorAtts.lightingFlag = 1
vis.PseudocolorAtts.minFlag = 1
vis.PseudocolorAtts.maxFlag = 1
vis.PseudocolorAtts.centering = vis.PseudocolorAtts.Natural # Natural, Nodal, Zonal
vis.PseudocolorAtts.scaling = vis.PseudocolorAtts.Linear # Linear, Log, Skew
vis.PseudocolorAtts.limitsMode = vis.PseudocolorAtts.CurrentPlot # OriginalData, CurrentPlot
vis.PseudocolorAtts.min = minVariableValue
vis.PseudocolorAtts.max = maxVariableValue
vis.PseudocolorAtts.pointSize = 0.05
vis.PseudocolorAtts.pointType = vis.PseudocolorAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.PseudocolorAtts.skewFactor = 1
vis.PseudocolorAtts.opacity = 1
vis.PseudocolorAtts.colorTableName = color_table
vis.PseudocolorAtts.invertColorTable = 0
vis.PseudocolorAtts.smoothingLevel = 0
vis.PseudocolorAtts.pointSizeVarEnabled = 0
vis.PseudocolorAtts.pointSizeVar = "default"
vis.PseudocolorAtts.pointSizePixels = 2
vis.PseudocolorAtts.lineStyle = vis.PseudocolorAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.PseudocolorAtts.lineWidth = 0
vis.PseudocolorAtts.opacityType = vis.PseudocolorAtts.Explicit # Explicit, ColorTable
vis.SetPlotOptions(vis.PseudocolorAtts)
vis.SetActivePlots(0)
vis.AddOperator("Slice", 1)
vis.AddOperator("Threshold", 1)
vis.ThresholdAtts = vis.ThresholdAttributes()
vis.ThresholdAtts.outputMeshType = 0
vis.ThresholdAtts.listedVarNames = ("Boundary_type")
vis.ThresholdAtts.zonePortions = (1)
vis.ThresholdAtts.lowerBounds = (1)
vis.ThresholdAtts.upperBounds = (1)
vis.ThresholdAtts.defaultVarName = variableName
vis.ThresholdAtts.defaultVarIsScalar = 1
vis.SetOperatorOptions(vis.ThresholdAtts, 1)
vis.ThresholdAtts = vis.ThresholdAttributes()
vis.ThresholdAtts.outputMeshType = 0
vis.ThresholdAtts.listedVarNames = ("Boundary_type")
vis.ThresholdAtts.zonePortions = (1)
vis.ThresholdAtts.lowerBounds = (1)
vis.ThresholdAtts.upperBounds = (1)
vis.ThresholdAtts.defaultVarName = variableName
vis.ThresholdAtts.defaultVarIsScalar = 1
vis.SetOperatorOptions(vis.ThresholdAtts, 1)
vis.SetActivePlots(0)
vis.SliceAtts = vis.SliceAttributes()
vis.SliceAtts.originType = vis.SliceAtts.Intercept # Point, Intercept, Percent, Zone, Node
vis.SliceAtts.originPoint = (0, 0, 0)
vis.SliceAtts.originIntercept = 0
vis.SliceAtts.originPercent = 0
vis.SliceAtts.originZone = 0
vis.SliceAtts.originNode = 0
vis.SliceAtts.normal = (0, 0, 1)
vis.SliceAtts.axisType = vis.SliceAtts.ZAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
vis.SliceAtts.upAxis = (0, 1, 0)
vis.SliceAtts.project2d = 1
vis.SliceAtts.interactive = 1
vis.SliceAtts.flip = 0
vis.SliceAtts.originZoneDomain = 0
vis.SliceAtts.originNodeDomain = 0
vis.SliceAtts.meshName = "SpatialGrid"
vis.SliceAtts.theta = 0
vis.SliceAtts.phi = 90
vis.SetOperatorOptions(vis.SliceAtts, 1)
vis.DrawPlots()
if endFrame == -1:
endFrame = vis.TimeSliderGetNStates() - 1
if startFrame == -1:
startFrame = 0
# Iterate through frames
for i in xrange(startFrame, endFrame + 1):
vis.SetTimeSliderState(i)
frame = i - startFrame
vis.View2DAtts = vis.View2DAttributes()
vis.View2DAtts.windowCoords = (startX + frame * dx, endX + frame * dx,
startY + frame * dy, endY + frame * dy)
vis.View2DAtts.viewportCoords = (0.2, 0.95, 0.15, 0.95)
vis.View2DAtts.fullFrameActivationMode = vis.View2DAtts.Auto # On, Off, Auto
vis.View2DAtts.fullFrameAutoThreshold = 100
vis.View2DAtts.xScale = vis.View2DAtts.LINEAR # LINEAR, LOG
vis.View2DAtts.yScale = vis.View2DAtts.LINEAR # LINEAR, LOG
vis.View2DAtts.windowValid = 1
vis.SetView2D(vis.View2DAtts)
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = outputDir
vis.SaveWindowAtts.fileName = outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = 1024
vis.SaveWindowAtts.height = 1024
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
# Make the movie:
framerate = 7
subprocess.call([
pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh",
outputDir, outputFileName, framerate
])
# need to run with Python 2 (e.g., python2)
import sys
sys.path.append(
"/home/robertsj/opt/visit/visit2_13_2.linux-x86_64/2.13.2/linux-x86_64/lib/site-packages/"
)
import visit
visit.Launch()
visit.ShowAllWindows()
visit.OpenDatabase("/home/robertsj/opt/visit/visit_data_files/CThead_mid.silo")
visit.AddPlot("Volume", "head")
visit.AddOperator("Slice")
s = visit.SliceAttributes()
s.originType = s.Intercept
s.axisType = s.ZAxis
s.originIntercept = 60.0
visit.SetOperatorOptions(s)
visit.DrawPlots()
visit.SaveWindow()
def visit_plot_qcrit_wx_3d_direct(xdmf_path,
wx_range=(-5.0, 5.0),
q_value=0.1,
config_view=None,
out_dir=os.getcwd(),
out_prefix='qcrit_wx_',
figsize=(1024, 1024),
state=None,
states=None,
states_range=[0, None, 1]):
visit_initialize()
visit.OpenDatabase(str(xdmf_path), 0)
# Add a pseudocolor of the cell-centered streamwise vorticity.
visit.AddPlot('Pseudocolor', 'wx_cc', 1, 1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag = 1
PseudocolorAtts.min = wx_range[0]
PseudocolorAtts.maxFlag = 1
PseudocolorAtts.max = wx_range[1]
PseudocolorAtts.colorTableName = 'viridis'
PseudocolorAtts.invertColorTable = 0
PseudocolorAtts.opacityType = PseudocolorAtts.Constant
PseudocolorAtts.opacity = 0.8
PseudocolorAtts.legendFlag = 0
visit.SetPlotOptions(PseudocolorAtts)
# Add an isosurface of the Q-criterion.
visit.AddOperator('Isosurface', 1)
IsosurfaceAtts = visit.IsosurfaceAttributes()
IsosurfaceAtts.variable = 'qcrit'
IsosurfaceAtts.contourMethod = IsosurfaceAtts.Value
IsosurfaceAtts.contourValue = (q_value)
IsosurfaceAtts.scaling = IsosurfaceAtts.Linear
visit.SetOperatorOptions(IsosurfaceAtts, 1)
# Remove info about user, time, database, and legend.
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.userInfoFlag = 0
AnnotationAtts.databaseInfoFlag = 0
AnnotationAtts.timeInfoFlag = 0
AnnotationAtts.legendInfoFlag = 0
AnnotationAtts.axes3D.visible = 0
AnnotationAtts.axes3D.triadFlag = 1
AnnotationAtts.axes3D.bboxFlag = 0
visit.SetAnnotationAttributes(AnnotationAtts)
# Parse the 3D view configuration file.
if config_view is not None:
View3DAtts = visit_get_view(config_view, '3D')
visit.SetView3D(View3DAtts)
visit.SetActiveWindow(1)
states = visit_get_states(state=state,
states=states,
states_range=states_range)
visit_render_save_states(states,
out_dir=out_dir,
out_prefix=out_prefix,
figsize=figsize)
visit_finalize()
return
Vi.HideActivePlots()
# Create the plot of the cube by activating the mesh and pseudocolor plots.
Vi.SetActivePlots((0, 1))
# Set the view normal to the first octant.
v = Vi.GetView3D()
v.viewNormal = (1, 1, 1)
Vi.SetView3D(v)
# Apply a clip through the first octant.
Vi.AddOperator("Clip")
c = Vi.ClipAttributes()
c.plane1Origin = (40, 40, 40)
c.plane1Normal = (1, 1, 1)
Vi.SetOperatorOptions(c)
# Include the CNERG logo in the bottom left corner of the plot.
image = Vi.CreateAnnotationObject("Image")
image.image = os.path.dirname(os.path.abspath(__file__)) + "/cnerg.jpg"
image.position = (0.02, 0.02)
image.width = 10
image.height = 10
Vi.DrawPlots()
if images:
Vi.SaveWindow()
# Create the second plot of the XY plane slice.
plane_slice_plotting(2, 2, "XY Plane", images)
def make_moving_frame_of_reference_line_plot(point1,
point2,
velocity,
variable_name,
input_directory,
input_file_name,
output_directory,
output_file_name,
start_frame=-1,
end_frame=-1,
frame_skip_dt=1.0):
'''
Function for making a line plot of some variable with a moving frame of reference
:param point1 The starting point of the line (must be an array of size 3)
:param point2 The ending point of the line (must be an array of size 3)
:param velocity The velocity vector of the frame of reference (must be an array of size 3)
:param variable_name Name of the variable (For ex \"rho\")
:param input_directory The path to the directory where the files are
:param input_file_name Name of the files (For ex \"bulk.*.silo\")
:param output_directory Directory where to output the movie
:param output_file_name Name of the outputted file (For ex \"RHOMOVIE\")
:param start_frame Starting frame for the movie (if -1, equals 0, -1 by default)
:param end_frame Ending frame for the movie (if -1, equals the last frame, -1 by default)
:param frame_skip_dt The number of seconds one skip in frame equals (1.0 by default) (Note: This may change depending on the run and should always be checked)
'''
if len(point1) != 3 or len(point2) != 3 or len(velocity) != 3:
print "BAD INPUT IN make_moving_frame_of_reference_line_plot, POINT1, POINT2 AND VELOCITY MUST BE ARRAYS OF SIZE 3"
# OPTIONS
#################################################################
# Input the boundary box for starting coordinates (Starting values)
startX = point1[0] # The left x-boundary of the box
endX = point2[0] # The right x-boundary of the box
startY = point1[1] # The bottom y-boundary of the box
endY = point2[1] # The upper y-boundary of the box
startZ = poin1[2] # The left z-boundary of the box
endZ = point2[2] # The right z-boundary of the box
# Input frame properties
startFrame = start_frame # Note: if startFrame is set to -1 the start frame gets set to 0
endFrame = end_frame # Note: if endFrame is set to -1 the endFrame is automatically the number of frames in the database
frameInSeconds = frame_skip_dt # Set how many seconds one frame skip is
screenWidth = 3000
screenHeight = 3000
# Input speed in x and y direction
speedX = velocity[0] # Meters per second
speedY = velocity[1] # Meters per second
speedZ = velocity[2] # Meters per second
# Input variable name
# Note: needs to have operators/Lineout/ for visit to recognize it as line plot. Additionally, visit does not accept any '/' in the variable name which is why they're removed. The curve definitions are in loadvisitsettings.py and in there the curve expressions are defined so that there's no '/' in the variable name
variableName = "operators/Lineout/" + variable_name.replace("/", "")
# Input directory and file names
outputDir = output_directory # Set the output directory (Where .png s are saved)
outputFileName = output_file_name # The file names for the png files. These for ex. will be saved visit0000.png, visit0001.png, ..
databaseName = "localhost:" + input_directory + input_file_name + " database" # For navigating to the silo files
# visitBinDirectory = "/usr/lvariableNameocal/visit/bin" #Nevermind this
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
dx = speedX * frameInSeconds # Note: This is in meters per frame!
dy = speedY * frameInSeconds # Note: This is in meters per frame!
dz = speedZ * frameInSeconds # Note: This is in meters per frame!
vis.OpenDatabase(databaseName, 0)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Curve", variableName, 1, 1)
vis.LineoutAtts = vis.LineoutAttributes()
vis.LineoutAtts.point1 = (startX, startY, 0)
vis.LineoutAtts.point2 = (endX, endY, 0)
vis.LineoutAtts.interactive = 0
vis.LineoutAtts.ignoreGlobal = 0
vis.LineoutAtts.samplingOn = 0
vis.LineoutAtts.numberOfSamplePoints = 50
vis.LineoutAtts.reflineLabels = 0
vis.SetOperatorOptions(vis.LineoutAtts, 1)
vis.CurveAtts = vis.CurveAttributes()
vis.CurveAtts.showLines = 1
vis.CurveAtts.lineStyle = vis.CurveAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.CurveAtts.lineWidth = 2
vis.CurveAtts.showPoints = 1
vis.CurveAtts.symbol = vis.CurveAtts.Point # Point, TriangleUp, TriangleDown, Square, Circle, Plus, X
vis.CurveAtts.pointSize = 5
vis.CurveAtts.pointFillMode = vis.CurveAtts.Static # Static, Dynamic
vis.CurveAtts.pointStride = 1
vis.CurveAtts.symbolDensity = 50
vis.CurveAtts.curveColorSource = vis.CurveAtts.Custom # Cycle, Custom
vis.CurveAtts.curveColor = (0, 0, 0, 255)
vis.CurveAtts.showLegend = 1
vis.CurveAtts.showLabels = 0
vis.CurveAtts.designator = ""
vis.CurveAtts.doBallTimeCue = 0
vis.CurveAtts.ballTimeCueColor = (0, 0, 0, 255)
vis.CurveAtts.timeCueBallSize = 0.01
vis.CurveAtts.doLineTimeCue = 0
vis.CurveAtts.lineTimeCueColor = (0, 0, 0, 255)
vis.CurveAtts.lineTimeCueWidth = 0
vis.CurveAtts.doCropTimeCue = 0
vis.CurveAtts.timeForTimeCue = 0
vis.SetPlotOptions(vis.CurveAtts)
vis.DrawPlots()
# Iterate through frames
for i in xrange(startFrame, endFrame + 1):
vis.SetTimeSliderState(i)
frame = i - startFrame
vis.LineoutAtts = vis.LineoutAttributes()
vis.LineoutAtts.point1 = (startX + frame * dx, startY + frame * dy, 0)
vis.LineoutAtts.point2 = (endX + frame * dx, endY + frame * dy, 0)
vis.LineoutAtts.interactive = 0
vis.LineoutAtts.ignoreGlobal = 0
vis.LineoutAtts.samplingOn = 0
vis.LineoutAtts.numberOfSamplePoints = 50
vis.LineoutAtts.reflineLabels = 0
vis.SetOperatorOptions(vis.LineoutAtts, 1)
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = outputDir
vis.SaveWindowAtts.fileName = outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = screenWidth
vis.SaveWindowAtts.height = screenHeight
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 80
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
# Make the movie:
framerate = 5
subprocess.call([
pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh",
outputDir, outputFileName, framerate
])
Zs = np.linspace(Zmin, Zmax, num=N)
visit.AddPlot("Pseudocolor", "vol_frac_average", 1, 1)
visit.AddOperator("Clip", 1)
ClipAtts = visit.ClipAttributes()
ClipAtts.quality = ClipAtts.Fast # Fast, Accurate
ClipAtts.funcType = ClipAtts.Plane # Plane, Sphere
ClipAtts.plane1Status = 1
ClipAtts.plane2Status = 0
ClipAtts.plane3Status = 0
ClipAtts.plane1Origin = (0, 0, 0)
ClipAtts.plane1Normal = (0, 1, 0)
ClipAtts.planeInverse = 1
ClipAtts.planeToolControlledClipPlane = ClipAtts.Plane1 # None, Plane1, Plane2, Plane3
visit.SetOperatorOptions(ClipAtts, 1)
visit.AddOperator("Slice", 1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag = 1
PseudocolorAtts.min = 0.
PseudocolorAtts.maxFlag = 1
PseudocolorAtts.max = 0.05
visit.SetPlotOptions(PseudocolorAtts)
SliceAtts = visit.SliceAttributes()
SliceAtts.originType = SliceAtts.Point
SliceAtts.normal = (-1, 0, 0)
SliceAtts.axisType = SliceAtts.XAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
SliceAtts.upAxis = (0, 1, 0)
SliceAtts.project2d = 1
def create_visit_point_movie(variableName,
minValue,
maxValue,
inputDirectory,
inputFileNames,
coordinates,
outputDirectory,
outputFileName,
colorTable="hot_desaturated"):
'''
Function for making a movie
Arguments:
:param variableName Name of the variable
:param minValue Minimum value of the variable
:param maxValue Maximum value of the variable
:param inputDirectory Path to input vlsv/silo files
:param inputFileNames Name of the files for example [\"bulk.00000.silo\", \"bulk.00001.silo\"]
:param coordinates Coordinates corresponding to the files so for example [ [[0,0,0], [0,1,0]], [[2,1,2], [2,1,4]] ]
:param outputDirectory Path to output directory
:param outputFileName Name of the output file
:param colorTable="hot_desaturated" Color table for the plots
'''
coordinates = [coordinates]
for i in range(len(inputFileNames)):
# OPTIONS
#################################################################
# Input variable
_variableName = variableName
minVariableValue = minValue
maxVariableValue = maxValue
colorTableName = colorTable
# Input directory and file names
#_outputDir = "/home/hannukse/MOVINGFRAME_MOVIES/AAJ_BZ_REMAKE/" # Set the output directory (Where .png s are saved)
_outputDir = outputDirectory
#_outputFileName = "BZ_FORESHOCK_2_" # The file names for the png files. These for ex. will be saved visit0000.png, visit0001.png, ..
_outputFileName = outputFileName # The file names for the png files.
#databaseName = "localhost:/home/hannukse/meteo/stornext/field/vlasiator/2D/AAJ/silo_files/bulk.*.silo database" # For navigating to the silo files
inputFileName = inputFileNames[i]
databaseName = "localhost:" + inputDirectory + inputFileName # For navigating to the silo files
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
# LaunchNowin(vdir=visitBinDirectory)
#dx = speedX * frameInSeconds # Note: This is in meters per frame!
#dy = speedY * frameInSeconds # Note: This is in meters per frame!
#LaunchNowin(vdir="/usr/local/visit/bin")
#Set up window and annotations
#vis.LaunchNowin(vdir="/usr/local/visit/bin")
inputFileName2 = "point.vtk"
databaseName2 = "localhost:" + os.getcwd() + "/" + inputFileName2
vis.OpenDatabase(databaseName, 0)
#vis.ActiveDatabase("localhost:" + inputDirectory + inputFileName)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Pseudocolor", _variableName, 1, 1) #CONTINUE
vis.SetActivePlots(1)
vis.PseudocolorAtts = vis.PseudocolorAttributes()
vis.PseudocolorAtts.legendFlag = 1
vis.PseudocolorAtts.lightingFlag = 1
vis.PseudocolorAtts.minFlag = 1
vis.PseudocolorAtts.maxFlag = 1
vis.PseudocolorAtts.centering = vis.PseudocolorAtts.Natural # Natural, Nodal, Zonal
vis.PseudocolorAtts.scaling = vis.PseudocolorAtts.Linear # Linear, Log, Skew
vis.PseudocolorAtts.limitsMode = vis.PseudocolorAtts.CurrentPlot # OriginalData, CurrentPlot
vis.PseudocolorAtts.min = minVariableValue
vis.PseudocolorAtts.max = maxVariableValue
vis.PseudocolorAtts.pointSize = 0.05
vis.PseudocolorAtts.pointType = vis.PseudocolorAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.PseudocolorAtts.skewFactor = 1
vis.PseudocolorAtts.opacity = 1
vis.PseudocolorAtts.colorTableName = colorTableName
vis.PseudocolorAtts.invertColorTable = 0
vis.PseudocolorAtts.smoothingLevel = 0
vis.PseudocolorAtts.pointSizeVarEnabled = 0
vis.PseudocolorAtts.pointSizeVar = "default"
vis.PseudocolorAtts.pointSizePixels = 2
vis.PseudocolorAtts.lineStyle = vis.PseudocolorAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.PseudocolorAtts.lineWidth = 0
vis.PseudocolorAtts.opacityType = vis.PseudocolorAtts.Explicit # Explicit, ColorTable
vis.SetPlotOptions(vis.PseudocolorAtts)
vis.SetActivePlots(1)
vis.AddOperator("Slice", 1)
vis.SetActivePlots(1)
vis.SliceAtts = vis.SliceAttributes()
vis.SliceAtts.originType = vis.SliceAtts.Intercept # Point, Intercept, Percent, Zone, Node
vis.SliceAtts.originPoint = (0, 0, 0)
vis.SliceAtts.originIntercept = 0
vis.SliceAtts.originPercent = 0
vis.SliceAtts.originZone = 0
vis.SliceAtts.originNode = 0
vis.SliceAtts.normal = (0, 0, 1)
vis.SliceAtts.axisType = vis.SliceAtts.ZAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
vis.SliceAtts.upAxis = (0, 1, 0)
vis.SliceAtts.project2d = 1
vis.SliceAtts.interactive = 1
vis.SliceAtts.flip = 0
vis.SliceAtts.originZoneDomain = 0
vis.SliceAtts.originNodeDomain = 0
vis.SliceAtts.meshName = "SpatialGrid"
vis.SliceAtts.theta = 0
vis.SliceAtts.phi = 90
vis.SetOperatorOptions(vis.SliceAtts, 1)
vis.DrawPlots()
vis.SetActivePlots(0)
for coordinate in coordinates[i]:
print(str(coordinate))
create_point_vtk(fileName=inputFileName2, coordinates=coordinate)
vis.OpenDatabase(databaseName2, 0)
vis.AddPlot("Mesh", "mesh", 1, 1)
vis.SetActivePlots(vis.GetNumPlots())
vis.MeshAtts = vis.MeshAttributes()
vis.MeshAtts.legendFlag = 1
vis.MeshAtts.lineStyle = vis.MeshAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.MeshAtts.lineWidth = 0
vis.MeshAtts.meshColor = (0, 0, 0, 255)
vis.MeshAtts.outlineOnlyFlag = 0
vis.MeshAtts.errorTolerance = 0.01
vis.MeshAtts.meshColorSource = vis.MeshAtts.Foreground # Foreground, MeshCustom
vis.MeshAtts.opaqueColorSource = vis.MeshAtts.Background # Background, OpaqueCustom
vis.MeshAtts.opaqueMode = vis.MeshAtts.Auto # Auto, On, Off
vis.MeshAtts.pointSize = 0.05
vis.MeshAtts.opaqueColor = (255, 255, 255, 255)
vis.MeshAtts.smoothingLevel = vis.MeshAtts.None # None, Fast, High
vis.MeshAtts.pointSizeVarEnabled = 0
vis.MeshAtts.pointSizeVar = "default"
vis.MeshAtts.pointType = vis.MeshAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.MeshAtts.showInternal = 0
vis.MeshAtts.pointSizePixels = 10
vis.MeshAtts.opacity = 1
vis.SetPlotOptions(vis.MeshAtts)
vis.DrawPlots()
# Iterate through frames
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = _outputDir
vis.SaveWindowAtts.fileName = _outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = 3000
vis.SaveWindowAtts.height = 3000
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
vis.CloseDatabase(databaseName2)
# Make the movie:
#subprocess.call("./moviecompilescript.sh " + _outputDir + " " + _outputFileName)
pyVisitPath = "pyVisit/"
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh")
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh " + _outputDir + " " + _outputFileName)
framerate = "10"
subprocess.call([
pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh",
_outputDir, _outputFileName, framerate
])
# Delete the point vtk file:
os.remove(os.getcwd() + "/" + inputFileName2)
def visit_plot_qcrit_wx_3d(xdmf_dir,
wx_range=(-5.0, 5.0),
q_value=0.1,
config_view=None,
out_dir=os.getcwd(),
out_prefix='wake3d_',
figsize=(1024, 1024),
visit_dir=None,
visit_arch='linux-x86_64',
state=None,
states=None,
states_range=[0, None, 1]):
# Import VisIt package.
if visit_dir is None:
visit_dir = os.environ.get('VISIT_DIR')
if visit_dir is None:
raise ValueError('Provide VisIt installation path or '
'set env variable VISIT_DIR')
sys.path.append(os.path.join(visit_dir, visit_arch, 'lib',
'site-packages'))
import visit
visit.LaunchNowin()
# Check version of VisIt.
visit_check_version(visit.Version())
# Define some variables to get the q_crit and wx_cc.
p_xdmf_path = os.path.join(str(xdmf_dir), 'p.xmf')
visit.OpenDatabase(p_xdmf_path, 0)
visit.DefineScalarExpression("operators/ConnectedComponents/p Grid",
"cell_constant(<p Grid>, 0.)")
visit.DefineCurveExpression("operators/DataBinning/1D/p Grid",
"cell_constant(<p Grid>, 0)")
visit.DefineScalarExpression("operators/DataBinning/2D/p Grid",
"cell_constant(<p Grid>, 0)")
visit.DefineScalarExpression("operators/DataBinning/3D/p Grid",
"cell_constant(<p Grid>, 0)")
visit.DefineScalarExpression("operators/Flux/p Grid",
"cell_constant(<p Grid>, 0.)")
visit.DefineCurveExpression("operators/Lineout/p",
"cell_constant(<p>, 0.)")
visit.DefineCurveExpression(
"operators/Lineout/time_derivative/p Grid_time",
"cell_constant(time_derivative/p Grid_time, 0.)")
visit.DefineCurveExpression(
"operators/Lineout/time_derivative/p Grid_lasttime",
"cell_constant(time_derivative/p Grid_lasttime, 0.)")
visit.DefineCurveExpression("operators/Lineout/time_derivative/p",
"cell_constant(time_derivative/p, 0.)")
visit.DefineScalarExpression("operators/ModelFit/model",
"point_constant(<p Grid>, 0)")
visit.DefineScalarExpression("operators/ModelFit/distance",
"point_constant(<p Grid>, 0)")
visit.DefineScalarExpression("operators/StatisticalTrends/Sum/p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression("operators/StatisticalTrends/Mean/p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression("operators/StatisticalTrends/Variance/p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression("operators/StatisticalTrends/Std. Dev./p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression("operators/StatisticalTrends/Slope/p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression("operators/StatisticalTrends/Residuals/p",
"cell_constant(<p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Sum/time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Sum/time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Sum/time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Mean/time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Mean/time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Mean/time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Variance/time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Variance/time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Variance/time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Std. Dev./time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Std. Dev./time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Std. Dev./time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Slope/time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Slope/time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Slope/time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Residuals/time_derivative/p Grid_time",
"cell_constant(<time_derivative/p Grid_time>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Residuals/time_derivative/p Grid_lasttime",
"cell_constant(<time_derivative/p Grid_lasttime>, 0.)")
visit.DefineScalarExpression(
"operators/StatisticalTrends/Residuals/time_derivative/p",
"cell_constant(<time_derivative/p>, 0.)")
visit.DefineVectorExpression("operators/SurfaceNormal/p Grid",
"cell_constant(<p Grid>, 0.)")
# Define cell-centered velocity vector field.
ux_xdmf_path = os.path.join(str(xdmf_dir), 'u.xmf')
uy_xdmf_path = os.path.join(str(xdmf_dir), 'v.xmf')
uz_xdmf_path = os.path.join(str(xdmf_dir), 'w.xmf')
vel_exp = ('{' +
'pos_cmfe(<{}[0]id:u>, <p Grid>, 1.0),'.format(ux_xdmf_path) +
'pos_cmfe(<{}[0]id:v>, <p Grid>, 0.0),'.format(uy_xdmf_path) +
'pos_cmfe(<{}[0]id:w>, <p Grid>, 0.0)'.format(uz_xdmf_path) +
'}')
visit.DefineVectorExpression('velocity', vel_exp)
# Define Q-criterion.
qcrit_exp = ('q_criterion(' + 'gradient(velocity[0]),' +
'gradient(velocity[1]),' + 'gradient(velocity[2])' + ')')
visit.DefineScalarExpression('q_crit', qcrit_exp)
# Define cell-centered streamwise vorticity.
wx_xdmf_path = os.path.join(str(xdmf_dir), 'wx.xmf')
wx_exp = 'pos_cmfe(<{}[0]id:wx>, <p Grid>, 0.0)'.format(wx_xdmf_path)
visit.DefineScalarExpression('wx_cc', wx_exp)
# Add a pseudocolor of the cell-centered streamwise vorticity.
visit.AddPlot('Pseudocolor', 'wx_cc', 1, 1)
PseudocolorAtts = visit.PseudocolorAttributes()
PseudocolorAtts.minFlag = 1
PseudocolorAtts.min = wx_range[0]
PseudocolorAtts.maxFlag = 1
PseudocolorAtts.max = wx_range[1]
PseudocolorAtts.colorTableName = 'viridis'
PseudocolorAtts.invertColorTable = 1
PseudocolorAtts.opacityType = PseudocolorAtts.Constant
PseudocolorAtts.opacity = 0.8
PseudocolorAtts.legendFlag = 0
visit.SetPlotOptions(PseudocolorAtts)
# Add an isosurface of the Q-criterion.
visit.AddOperator('Isosurface', 1)
IsosurfaceAtts = visit.IsosurfaceAttributes()
IsosurfaceAtts.variable = 'q_crit'
IsosurfaceAtts.contourMethod = IsosurfaceAtts.Value
IsosurfaceAtts.contourValue = (q_value)
IsosurfaceAtts.scaling = IsosurfaceAtts.Linear
visit.SetOperatorOptions(IsosurfaceAtts, 1)
# Remove info about user, time, database, and legend.
AnnotationAtts = visit.AnnotationAttributes()
AnnotationAtts.userInfoFlag = 0
AnnotationAtts.databaseInfoFlag = 0
AnnotationAtts.timeInfoFlag = 0
AnnotationAtts.legendInfoFlag = 0
AnnotationAtts.axes3D.visible = 0
AnnotationAtts.axes3D.triadFlag = 1
AnnotationAtts.axes3D.bboxFlag = 0
visit.SetAnnotationAttributes(AnnotationAtts)
# Parse the 3D view configuration file.
if config_view is not None:
with open(str(config_view), 'r') as infile:
config_view = yaml.load(infile, Loader=yaml.FullLoader)
config_view = config_view['View3DAtts']
# Set attributes of the view.
View3DAtts = visit.View3DAttributes()
for key, value in config_view.items():
if type(value) is list:
value = tuple(value)
setattr(View3DAtts, key, value)
visit.SetView3D(View3DAtts)
visit.SetActiveWindow(1)
visit.Source(os.path.join(visit_dir, visit_arch, 'bin', 'makemovie.py'))
visit.ToggleCameraViewMode()
# Create output directory if necessary.
if not os.path.isdir(str(out_dir)):
os.makedirs(str(out_dir))
# Loop over the states to render and save the plots.
if state is not None:
states = [state]
elif states is None:
if states_range[1] is None:
states_range[1] = visit.TimeSliderGetNStates()
else:
states_range[1] += 1
states = range(*states_range)
for i, state in enumerate(states):
print('[state {}] Rendering and saving figure ...'.format(state))
visit.SetTimeSliderState(state)
if i == 0:
visit.DrawPlots()
RenderingAtts = visit.RenderingAttributes()
visit.SetRenderingAttributes(RenderingAtts)
SaveWindowAtts = visit.SaveWindowAttributes()
SaveWindowAtts.outputToCurrentDirectory = 0
SaveWindowAtts.outputDirectory = str(out_dir)
SaveWindowAtts.fileName = '{}{:0>4}'.format(out_prefix, state)
SaveWindowAtts.family = 0
SaveWindowAtts.format = SaveWindowAtts.PNG
SaveWindowAtts.width = figsize[0]
SaveWindowAtts.height = figsize[1]
SaveWindowAtts.quality = 100
SaveWindowAtts.resConstraint = SaveWindowAtts.NoConstraint
visit.SetSaveWindowAttributes(SaveWindowAtts)
visit.SaveWindow()
os.remove('visitlog.py')
visit.CloseComputeEngine()
visit.Close()
return
def draw_point_picture(variableName,
minValue,
maxValue,
inputDirectory,
inputFileName,
coordinate,
outputDirectory,
outputFileName,
colorTable="hot_desaturated"):
'''
Function for making a visit plot with a point
Arguments:
:param variableName Name of the variable
:param minValue Minimum value of the variable
:param maxValue Maximum value of the variable
:param inputDirectory Path to input vlsv/silo files
:param inputFileName Name of the file, for example \"bulk.00000.silo\"
:param coordinates Coordinates corresponding to the files so for example [ [[0,0,0], [0,1,0]], [[2,1,2], [2,1,4]] ]
:param outputDirectory Path to output directory
:param outputFileName Name of the output file
:param colorTable="hot_desaturated" Color table for the plots
'''
# OPTIONS
#################################################################
# Input variable
_variableName = variableName
minVariableValue = minValue
maxVariableValue = maxValue
colorTableName = colorTable
# Input directory and file names
_outputDir = outputDirectory
_outputFileName = outputFileName # The file names for the png files.
databaseName = "localhost:" + inputDirectory + inputFileName # For navigating to the silo files
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
inputFileName2 = "point.vtk"
databaseName2 = "localhost:" + os.getcwd() + "/" + inputFileName2
currentPlot = 0
vis.OpenDatabase(databaseName, 0)
#vis.ActiveDatabase("localhost:" + inputDirectory + inputFileName)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Pseudocolor", _variableName, 1, 1) #CONTINUE
vis.SetActivePlots(currentPlot)
vis.PseudocolorAtts = vis.PseudocolorAttributes()
vis.PseudocolorAtts.legendFlag = 1
vis.PseudocolorAtts.lightingFlag = 1
vis.PseudocolorAtts.minFlag = 1
vis.PseudocolorAtts.maxFlag = 1
vis.PseudocolorAtts.centering = vis.PseudocolorAtts.Natural # Natural, Nodal, Zonal
vis.PseudocolorAtts.scaling = vis.PseudocolorAtts.Linear # Linear, Log, Skew
vis.PseudocolorAtts.limitsMode = vis.PseudocolorAtts.CurrentPlot # OriginalData, CurrentPlot
vis.PseudocolorAtts.min = minVariableValue
vis.PseudocolorAtts.max = maxVariableValue
vis.PseudocolorAtts.pointSize = 0.05
vis.PseudocolorAtts.pointType = vis.PseudocolorAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.PseudocolorAtts.skewFactor = 1
vis.PseudocolorAtts.opacity = 1
vis.PseudocolorAtts.colorTableName = colorTableName
vis.PseudocolorAtts.invertColorTable = 0
vis.PseudocolorAtts.smoothingLevel = 0
vis.PseudocolorAtts.pointSizeVarEnabled = 0
vis.PseudocolorAtts.pointSizeVar = "default"
vis.PseudocolorAtts.pointSizePixels = 2
vis.PseudocolorAtts.lineStyle = vis.PseudocolorAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.PseudocolorAtts.lineWidth = 0
vis.PseudocolorAtts.opacityType = vis.PseudocolorAtts.Explicit # Explicit, ColorTable
vis.SetPlotOptions(vis.PseudocolorAtts)
vis.AddOperator("Slice", 1)
vis.SliceAtts = vis.SliceAttributes()
vis.SliceAtts.originType = vis.SliceAtts.Intercept # Point, Intercept, Percent, Zone, Node
vis.SliceAtts.originPoint = (0, 0, 0)
vis.SliceAtts.originIntercept = 0
vis.SliceAtts.originPercent = 0
vis.SliceAtts.originZone = 0
vis.SliceAtts.originNode = 0
vis.SliceAtts.normal = (0, 0, 1)
vis.SliceAtts.axisType = vis.SliceAtts.ZAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
vis.SliceAtts.upAxis = (0, 1, 0)
vis.SliceAtts.project2d = 1
vis.SliceAtts.interactive = 1
vis.SliceAtts.flip = 0
vis.SliceAtts.originZoneDomain = 0
vis.SliceAtts.originNodeDomain = 0
vis.SliceAtts.meshName = "SpatialGrid"
vis.SliceAtts.theta = 0
vis.SliceAtts.phi = 90
vis.SetOperatorOptions(vis.SliceAtts, 1)
vis.DrawPlots()
create_point_vtk(fileName=inputFileName2, coordinates=coordinate)
vis.OpenDatabase(databaseName2, 0)
currentPlot = currentPlot + 1
vis.SetActivePlots(currentPlot)
vis.AddPlot("Mesh", "mesh", 1, 1)
vis.MeshAtts = vis.MeshAttributes()
vis.MeshAtts.legendFlag = 1
vis.MeshAtts.lineStyle = vis.MeshAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.MeshAtts.lineWidth = 0
vis.MeshAtts.meshColor = (0, 0, 0, 255)
vis.MeshAtts.outlineOnlyFlag = 0
vis.MeshAtts.errorTolerance = 0.01
vis.MeshAtts.meshColorSource = vis.MeshAtts.Foreground # Foreground, MeshCustom
vis.MeshAtts.opaqueColorSource = vis.MeshAtts.Background # Background, OpaqueCustom
vis.MeshAtts.opaqueMode = vis.MeshAtts.Auto # Auto, On, Off
vis.MeshAtts.pointSize = 0.05
vis.MeshAtts.opaqueColor = (255, 255, 255, 255)
vis.MeshAtts.smoothingLevel = vis.MeshAtts.None # None, Fast, High
vis.MeshAtts.pointSizeVarEnabled = 0
vis.MeshAtts.pointSizeVar = "default"
vis.MeshAtts.pointType = vis.MeshAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.MeshAtts.showInternal = 0
vis.MeshAtts.pointSizePixels = 25
vis.MeshAtts.opacity = 1
vis.SetPlotOptions(vis.MeshAtts)
vis.DrawPlots()
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = _outputDir
vis.SaveWindowAtts.fileName = _outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = 3000
vis.SaveWindowAtts.height = 3000
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.SetActivePlots((0, 1))
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName2)
vis.CloseDatabase(databaseName)
def make_movie_auto(variableName,
boundaryBox,
vlsvFileName,
inputDirectory,
inputFileName,
outputDirectory,
outputFileName,
colorTableName="hot_desaturated",
startFrame=-1,
endFrame=-1,
thresholdCoefficient=0.6):
'''
Function for making a movie
Arguments:
:param variableName Name of the variable
:param boundaryBox Box for collecting min and max threshold (The movie will focus on that area)
:param vlsvFileName Name of a vlsv file where the function collects the threshold for the boundary box
:param inputDirectory Path to input vlsv/silo files
:param inputFileName Name of the file(s) so for example if the filenames are bulk.0000.silo, bulk.0001.silo, .. then inputFileName=\"bulk.*.silo\""
:param outputDirectory Path to output directory
:param outputFileName Name of the output file
:param colorTableName="hot_desaturated" Color table for the plots
:param thresholdCoefficient Sets the coefficient for a covariant collected from the values from boundary box. The lower this is, the more focused the movie will be on the boundary box area
:param startFrame=-1 Starting frame of the movie (-1 equals 0)
:param endFrame=-1 Starting frame of the movie (-1 equals last frame)
'''
if thresholdCoefficient < 0:
print("thresholdCoefficient must be non-negative!")
return
# OPTIONS
#################################################################
# Input frame properties
_startFrame = startFrame # Note: if _startFrame is set to -1 the start frame gets set to 0
_endFrame = endFrame # Note: if _endFrame is set to -1 the _endFrame is automatically the number of frames in the database
# Input variable
_variableName = variableName
# Input directory and file names
#_outputDir = "/home/hannukse/MOVINGFRAME_MOVIES/AAJ_BZ_REMAKE/" # Set the output directory (Where .png s are saved)
_outputDir = outputDirectory
#_outputFileName = "BZ_FORESHOCK_2_" # The file names for the png files. These for ex. will be saved visit0000.png, visit0001.png, ..
_outputFileName = outputFileName # The file names for the png files.
#databaseName = "localhost:/home/hannukse/meteo/stornext/field/vlasiator/2D/AAJ/silo_files/bulk.*.silo database" # For navigating to the silo files
databaseName = "localhost:" + inputDirectory + inputFileName + " database" # For navigating to the silo files
# Note: a slice of the plot in z-axis is taken automatically
#################################################################
# Get the min and max values:
# Get all cell ids within the boundary box:
vlsvReader = VlsvReader(vlsvFileName)
# Get global boundaries:
# Get xmax, xmin and xcells_ini
xmax = vlsvReader.read_parameter(name="xmax")
xmin = vlsvReader.read_parameter(name="xmin")
xcells = vlsvReader.read_parameter(name="xcells_ini")
# Do the same for y
ymax = vlsvReader.read_parameter(name="ymax")
ymin = vlsvReader.read_parameter(name="ymin")
ycells = vlsvReader.read_parameter(name="ycells_ini")
# And for z
zmax = vlsvReader.read_parameter(name="zmax")
zmin = vlsvReader.read_parameter(name="zmin")
zcells = vlsvReader.read_parameter(name="zcells_ini")
#Calculate cell lengths:
cell_lengths = np.array([(xmax - xmin) / (float)(xcells),
(ymax - ymin) / (float)(ycells),
(zmax - zmin) / (float)(zcells)])
# Get cell indices:
cell_indice_bounds = np.array([
(int)(((float)(boundaryBox[0]) - xmin) / (float)(cell_lengths[0])),
(int)(((float)(boundaryBox[1]) - xmin) / (float)(cell_lengths[0])),
(int)(((float)(boundaryBox[2]) - ymin) / (float)(cell_lengths[1])),
(int)(((float)(boundaryBox[3]) - ymin) / (float)(cell_lengths[1])),
(int)(((float)(boundaryBox[4]) - zmin) / (float)(cell_lengths[2])),
(int)(((float)(boundaryBox[5]) - zmin) / (float)(cell_lengths[2]))
])
# Get every cell id within the boundary box:
cellids = []
cell_indice = np.array(
[cell_indice_bounds[0], cell_indice_bounds[2], cell_indice_bounds[4]])
while True:
cellids.append(cell_indice[0] + cell_indice[1] * xcells +
cell_indice[2] * xcells * ycells + 1)
if cell_indice[0] < cell_indice_bounds[1]:
cell_indice[0] = cell_indice[0] + 1
elif cell_indice[1] < cell_indice_bounds[3]:
cell_indice[1] = cell_indice[1] + 1
cell_indice[0] = cell_indice_bounds[0]
elif cell_indice[2] < cell_indice_bounds[5]:
cell_indice[2] = cell_indice[2] + 1
cell_indice[1] = cell_indice_bounds[1]
cell_indice[0] = cell_indice_bounds[0]
else:
# Indice out of bounds -- got all cell ids
break
# Convert cell ids into set:
cellids = Set(cellids)
cellidlocations = []
# Get all of the cell ids locations:
allcellids = vlsvReader.read(name="SpatialGrid", tag="MESH")
for i in range(len(allcellids)):
if allcellids[i] in cellids:
#This cell id is within the user-given boundary
cellidlocations.append(allcellids[i])
# Get all of the values:
allvalues = vlsvReader.read_variables(name=_variableName)
values = []
# Get the values of the cell ids within the boundary
for i in cellidlocations:
values.append(allvalues[i])
# We now have all the cell ids (and their locations in the arrays) from the area, set min and max thresholds:
meanValue = np.mean(values)
standardDeviationValue = np.std(values)
maxValue = meanValue + (
float)(thresholdCoefficient) * standardDeviationValue
minValue = meanValue - (
float)(thresholdCoefficient) * standardDeviationValue
# Put threshold values:
minVariableValue = minValue
maxVariableValue = maxValue
# LaunchNowin(vdir=visitBinDirectory)
#dx = speedX * frameInSeconds # Note: This is in meters per frame!
#dy = speedY * frameInSeconds # Note: This is in meters per frame!
#LaunchNowin(vdir="/usr/local/visit/bin")
#Set up window and annotations
#vis.LaunchNowin(vdir="/usr/local/visit/bin")
vis.OpenDatabase(databaseName, 0)
#Load settings
visSettings.load_visit_settings()
vis.AddPlot("Pseudocolor", _variableName, 1, 1) #CONTINUE
vis.SetActivePlots(0)
vis.PseudocolorAtts = vis.PseudocolorAttributes()
vis.PseudocolorAtts.legendFlag = 1
vis.PseudocolorAtts.lightingFlag = 1
vis.PseudocolorAtts.minFlag = 1
vis.PseudocolorAtts.maxFlag = 1
vis.PseudocolorAtts.centering = vis.PseudocolorAtts.Natural # Natural, Nodal, Zonal
vis.PseudocolorAtts.scaling = vis.PseudocolorAtts.Linear # Linear, Log, Skew
vis.PseudocolorAtts.limitsMode = vis.PseudocolorAtts.CurrentPlot # OriginalData, CurrentPlot
vis.PseudocolorAtts.min = minVariableValue
vis.PseudocolorAtts.max = maxVariableValue
vis.PseudocolorAtts.pointSize = 0.05
vis.PseudocolorAtts.pointType = vis.PseudocolorAtts.Point # Box, Axis, Icosahedron, Point, Sphere
vis.PseudocolorAtts.skewFactor = 1
vis.PseudocolorAtts.opacity = 1
vis.PseudocolorAtts.colorTableName = colorTableName
vis.PseudocolorAtts.invertColorTable = 0
vis.PseudocolorAtts.smoothingLevel = 0
vis.PseudocolorAtts.pointSizeVarEnabled = 0
vis.PseudocolorAtts.pointSizeVar = "default"
vis.PseudocolorAtts.pointSizePixels = 2
vis.PseudocolorAtts.lineStyle = vis.PseudocolorAtts.SOLID # SOLID, DASH, DOT, DOTDASH
vis.PseudocolorAtts.lineWidth = 0
vis.PseudocolorAtts.opacityType = vis.PseudocolorAtts.Explicit # Explicit, ColorTable
vis.SetPlotOptions(vis.PseudocolorAtts)
vis.SetActivePlots(0)
vis.AddOperator("Slice", 1)
vis.SetActivePlots(0)
vis.SliceAtts = vis.SliceAttributes()
vis.SliceAtts.originType = vis.SliceAtts.Intercept # Point, Intercept, Percent, Zone, Node
vis.SliceAtts.originPoint = (0, 0, 0)
vis.SliceAtts.originIntercept = 0
vis.SliceAtts.originPercent = 0
vis.SliceAtts.originZone = 0
vis.SliceAtts.originNode = 0
vis.SliceAtts.normal = (0, 0, 1)
vis.SliceAtts.axisType = vis.SliceAtts.ZAxis # XAxis, YAxis, ZAxis, Arbitrary, ThetaPhi
vis.SliceAtts.upAxis = (0, 1, 0)
vis.SliceAtts.project2d = 1
vis.SliceAtts.interactive = 1
vis.SliceAtts.flip = 0
vis.SliceAtts.originZoneDomain = 0
vis.SliceAtts.originNodeDomain = 0
vis.SliceAtts.meshName = "SpatialGrid"
vis.SliceAtts.theta = 0
vis.SliceAtts.phi = 90
vis.SetOperatorOptions(vis.SliceAtts, 1)
vis.DrawPlots()
if _endFrame == -1:
_endFrame = vis.TimeSliderGetNStates() - 1
if _startFrame == -1:
_startFrame = 0
# Iterate through frames
for i in range(_startFrame, _endFrame + 1):
vis.SetTimeSliderState(i)
frame = i - _startFrame
vis.SaveWindowAtts = vis.SaveWindowAttributes()
vis.SaveWindowAtts.outputToCurrentDirectory = 0
vis.SaveWindowAtts.outputDirectory = _outputDir
vis.SaveWindowAtts.fileName = _outputFileName
vis.SaveWindowAtts.family = 1
vis.SaveWindowAtts.format = vis.SaveWindowAtts.PNG # BMP, CURVE, JPEG, OBJ, PNG, POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA, VTK, PLY
vis.SaveWindowAtts.width = 3000
vis.SaveWindowAtts.height = 300
vis.SaveWindowAtts.screenCapture = 0
vis.SaveWindowAtts.saveTiled = 0
vis.SaveWindowAtts.quality = 100
vis.SaveWindowAtts.progressive = 0
vis.SaveWindowAtts.binary = 0
vis.SaveWindowAtts.stereo = 0
vis.SaveWindowAtts.compression = vis.SaveWindowAtts.PackBits # None, PackBits, Jpeg, Deflate
vis.SaveWindowAtts.forceMerge = 0
vis.SaveWindowAtts.resConstraint = vis.SaveWindowAtts.ScreenProportions # NoConstraint, EqualWidthHeight, ScreenProportions
vis.SaveWindowAtts.advancedMultiWindowSave = 0
vis.SetSaveWindowAttributes(vis.SaveWindowAtts)
vis.SaveWindow()
vis.DeleteActivePlots()
vis.CloseDatabase(databaseName)
# Make the movie:
#subprocess.call("./moviecompilescript.sh " + _outputDir + " " + _outputFileName)
pyVisitPath = "pyVisit/"
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh")
#subprocess.call(pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh " + _outputDir + " " + _outputFileName)
frameRate = "10"
subprocess.call([
pythonLibDirectoryPath + pyVisitPath + "moviecompilescript.sh",
_outputDir, _outputFileName, frameRate
])
import sys
# visit
sys.path.append("/home/neo/visit/2.11.0/linux-x86_64/lib/site-packages")
import visit as vs
vs.Launch()
vs.OpenDatabase("visit-data/noise.silo")
vs.AddPlot("Pseudocolor", "hardyglobal")
vs.AddOperator("Slice")
s = vs.SliceAttributes()
s.project2d = 0
s.originPoint = (0, 5, 0)
s.originType = s.Point
s.normal = (0, 1, 0)
s.upAxis = (-1, 0, 0)
vs.SetOperatorOptions(s)
vs.AddOperator("Reflect")
vs.DrawPlots()
# Now reflect before slicing. We’ll only get 1 slice plane
# instead of 2.
vs.DemoteOperator(1)
vs.DrawPlots()
d = input('Press anything to quit')
def visit_config(geometry_file, data_file, args):
"""
Convert geometry file to stl, convert data file to vtk, load each file
into VisIt, and create and load a session file containing four plot windows.
1) A cube with a slice through an octant.
2) XY plane slice through the centroid.
3) XZ plane slice through the centroid.
4) YZ plane slice through the centroid.
Each window has a mesh plot with the "STL_mesh" variable, a Pseudocolor plot
with the "TALLY_TAG" variable, and the second, third, and fourth windows have
Contour plots with the "ERROR_TAG" variable. If the user has indicated to,
launch VisIt and load the session file.
Input:
______
geometry_file: h5m file
User supplied geometry file.
data_file: h5m or vtk file
User supplied data file.
args: Namespace
User supplied geometry file location, data file location, and
indication if the user wants images of the plot windows with a
timestamp and the session file saved and opened in VisIt.
Returns:
________
None
"""
# Create a list of dictionaries indicating the data, plot, and variable in VisIt.
Files = [{
"file_name": data_file,
"plot_type": "Pseudocolor",
"data_tag": "TALLY_TAG"
}, {
"file_name": data_file,
"plot_type": "Contour",
"data_tag": "ERROR_TAG"
}, {
"file_name": geometry_file,
"plot_type": "Mesh",
"data_tag": "STL_mesh"
}]
# Launch VisIt and add appropriate plots.
Vi.LaunchNowin()
for file in Files:
Vi.OpenDatabase(file["file_name"])
Vi.AddPlot(file["plot_type"], file["data_tag"])
# Hide the contour plot in the first plot window.
Vi.SetActivePlots(1)
Vi.HideActivePlots()
# Create the plot of the cube by activating the mesh and pseudocolor plots.
Vi.SetActivePlots((0, 2))
# Set the view normal to the first octant.
v = Vi.GetView3D()
v.viewNormal = (1, 1, 1)
Vi.SetView3D(v)
# Apply a clip through the first octant.
Vi.AddOperator("Clip")
c = Vi.ClipAttributes()
c.plane1Origin = (40, 40, 40)
c.plane1Normal = (1, 1, 1)
Vi.SetOperatorOptions(c)
# Include the CNERG logo in the bottom left corner of the plot.
image = Vi.CreateAnnotationObject("Image")
image.image = os.path.dirname(os.path.abspath(__file__)) + "/cnerg.jpg"
image.position = (0.02, 0.02)
image.width = 10
image.height = 10
Vi.DrawPlots()
if args.images:
if args.timestamp:
attributes = Vi.GetAnnotationAttributes()
attributes.userInfoFlag = 0
Vi.SetAnnotationAttributes(attributes)
Vi.SaveWindow()
# Create the second plot of the XY plane slice.
plane_slice_plotting(2, 2, "XY Plane", args.images, args.timestamp)
# Create the third plot of the XZ plane slice.
plane_slice_plotting(3, 1, "XZ Plane", args.images, args.timestamp)
# Create the fourth plot of the YZ plane slice.
plane_slice_plotting(4, 0, "ZY Plane", args.images, args.timestamp)
# Display the four windows in a 2x2 grid.
Vi.SetWindowLayout(4)
# Save the session file with the default VisIt output to the current directory.
visit_output = "VisitDefaultOutput.session"
Vi.SaveSession(visit_output)
Vi.Close()
# Retrieve the path to the VisIt session file.
session_file_path = os.path.join(os.getcwd(), visit_output)
# If the user has indicated to, open the session file with the VisIt GUI.
if args.openvisit:
os.system("visit -sessionfile {} &".format(session_file_path))
# If the user has indicated to, remove the session file after VisIt has opened.
if not args.sessionfile:
os.system("sleep 10; rm {}".format(session_file_path))
timestep = str(aux[-1]).zfill(6)
visit.OpenDatabase(db)
for variable in variables:
i = 0
for location in locations:
i += 1
LineoutAtts = visit.LineoutAttributes()
LineoutAtts.point1 = location[0]
LineoutAtts.point2 = location[1]
LineoutAtts.samplingOn = 1
LineoutAtts.numberOfSamplePoints = 1000
visit.AddPlot("Curve", "operators/Lineout/" + variable)
visit.SetOperatorOptions(LineoutAtts, 1)
visit.DrawPlots()
e = visit.ExportDBAttributes()
e.filename = sim + '_' + case + '_' + timestep + '_' + variable
e.dirname = output_folder
e.db_type = "Curve2D"
visit.ExportDatabase(e)
visit.DeleteAllPlots()
visit.CloseDatabase(db)
