basic.py

#!/usr/bin/python
# Filename: basic.py
#
# Code by Martin Jucker, distributed under an MIT License
# Any publication benefitting from this piece of code should cite
# Jucker, M 2014. Scientific Visualisation of Atmospheric Data with ParaView.
# Journal of Open Research Software 2(1):e4, DOI: http://dx.doi.org/10.5334/jors.al
#
# Python interface for ParaView (www.paraview.org). Reads netCDF file on an arbitrary grid, including logarithmic coordinates and time evolution (if present). netCDF file needs to loosely correspond to Climate and Forecast (FC) conventions (https://en.wikipedia.org/wiki/Climate_and_Forecast_Metadata_Conventions).
# Also provides helper functions for common operations.

##### needed modules: paraview.simple, math #########################
from paraview.simple import *
from math import pi,log10

# some global constants
strPi = str(pi)[0:7]

##### define auxiliary functions ##################################

# define logarithmic coordinate conversion
def ConvertLogCoordString(pString, basis=1e3):
    """Logarithmic coordinate conversion in string form for Calculator filter.

    Output is the string to be used inside the Calculator filter:
    pString -- the coordinate to convert
    basis   -- basis (surface) pressure to normalize
    """
    expression = '-log10(abs(' + pString + ')/' + str(basis) + ')'
    return expression

# do the coordinate conversion inside a Calculator
def Cart2Log(src=GetActiveSource(), ratios=[1,1,1], logCoords=[], basis=[]):
    """Convert between logarithmic and linear coordinates. Also applies aspect ratio correction.

    Adds a Calculator filter to the pipeline
    src       -- filter in pipeline to attach to
    ratios    -- multiplicative factor for coordinates - must be same length as # of dimensions
    logCoords -- indices (0 based) of coordinates to be converted
    basis     -- basis to normalize argument to logarithm (ie defines origin) - must be length 1 or same as logCoords
    """
    nVec=['iHat*','jHat*','kHat*']
    coords=['coordsX','coordsY','coordsZ']
    cFun=coords[:]
    pFun=''
    for pp in range(len(logCoords)):
        ci = logCoords[pp]
        if len(basis) == 1:
            bas = basis[0]
        else:
            bas = basis[pp]
        cFun[ci] = ConvertLogCoordString(coords[ci], bas)
    for ii in range(len(ratios)):
        if ratios[ii] != 1.0:
            pFun += nVec[ii]+cFun[ii] + '*'+str(ratios[ii]) + ' + '
        else:
            pFun += nVec[ii]+cFun[ii] + ' + '
    calc=Calculator(src)
    calc.Function = pFun[:-3]
    calc.CoordinateResults = 1
    return calc
# convert cartesian coordinates to spherical coordinates
def Cart2Spherical(radius=1.0, src=GetActiveSource()):
    """Convert Cartesian to spherical coordinates.

    Assumes X coordinate is longitude, Y coordinate latitude, Z coordinate vertical.
    Adds Calculator filter to the pipeline.
    radius -- radius of the sphere, where coordZ = basis
    src    -- filter in pipeline to attach to
    """
    calc=Calculator(src)
    strRad = str(radius)
    try:
        calc.Function = 'iHat*('+strRad+'+coordsZ)*cos(coordsY*'+strPi+'/180)*cos(coordsX*'+strPi+'/180) + jHat*('+strRad+'+coordsZ)*cos(coordsY*'+strPi+'/180)*sin(coordsX*'+strPi+'/180) + kHat*('+strRad+'+coordsZ)*sin(coordsY*'+strPi+'/180)'
    except:
        calc.Function = 'iHat*'+strRad+'*cos(coordsY*'+strPi+'/180)*cos(coordsX*'+strPi+'/180) + jHat*'+strRad+'*cos(coordsY*'+strPi+'/180)*sin(coordsX*'+strPi+'/180) + kHat*'+strRad+'*sin(coordsY*'+strPi+'/180)'
    calc.CoordinateResults = 1
    RenameSource('Cart2Spherical',calc)
    return calc

# apply aspect ratios to grid. This might already be done in Cart2Log
def GridAspectRatio(ratios, src=GetActiveSource()):
    """Adjust aspect ratio of Cartesian grid: multiplies ratios x coordinates.

    Adds Calculator filter to the pipeline.
    ratios -- 2- or 3-vector with multiplicative factors for each spatial coordinate
    """
    calc=Calculator(src)
    if len(ratios) == 1:
        calc.Function = 'iHat*'+str(ratios[0])+'*coordsX'
    elif len(ratios) == 2:
        calc.Function = 'iHat*'+str(ratios[0])+'*coordsX + jHat*'+str(ratios[1])+'*coordsY'
    elif len(ratios) == 3:
        calc.Function = 'iHat*'+str(ratios[0])+'*coordsX + jHat*'+str(ratios[1])+'*coordsY + kHat*'+str(ratios[2])+'*coordsZ'
    else:
        raise ValueError('Aspect ratios must be length 1,2 or 3, but is '+str(len(rations)))
    calc.CoordinateResults = 1
    return calc

# transform coordinates: logarithmic, aspect ratio
def TransformCoords(src=GetActiveSource(), aspectRatios=[1,1,1], logCoords=[], basis=[], reverseCoords=[], revCenter=[]):
    """Transform the coordinates depending on whether or not there are logarithmic coordinates"""
    if len(reverseCoords)>0:
        nVec = ['iHat*','jHat*','kHat*']
        nCoor= ['X','Y','Z']
        revCoor = Calculator(src)
        rFun = ''
        for dim in range(3):
            if dim in reverseCoords or -dim in reverseCoords:
                for d in range(len(reverseCoords)):
                    if dim == abs(reverseCoords[d]):
                        rd = d
                if reverseCoords[rd]<0:
                    coorSign = '+'
                else:
                    coorSign = '-'
                rFun += ' +'+nVec[dim]+'('+str(revCenter[rd])+coorSign+'coords'+nCoor[dim]+')'
            else:
                rFun += ' +'+nVec[dim]+'coords'+nCoor[dim]
        revCoor.Function = rFun[2:]
        revCoor.CoordinateResults = 1
        src = revCoor
    if len(logCoords)>0 :
        transCoor = Cart2Log(src=src,ratios=aspectRatios,logCoords=logCoords,basis=basis)
    else:
        transCoor = GridAspectRatio(ratios=aspectRatios, src=src)
    return transCoor

#
def MakeSelectable(src=GetActiveSource()):
    """Make filter selectable in pipeline browser, but don't show it."""
    rep=Show(src)
    rep.Visibility=0


######### read in data, redefine pressure coordinates and change aspect ratio ###############

def LoadData( fileName, ncDims=['lon','lat','pfull'], aspectRatios=[1,1,1], logCoords=[], basis=[], reverseCoords=[], revCenter=[], replaceNaN=True ):
    """Load netCDF file, convert coordinates into useful aspect ratio.

    Adds file output_nc, and Calculator LogP or Calculator AspRat to the pipeline

    INPUTS:
        fileName      -- full path and file name of data to be read
        ncDims        -- names of the dimensions within the netCDF file. Time should be excluded. Ordering [x,y,z]
        aspectRatios  -- how to scale coordinates [xscale,yscale,zscale]. Z coordinate is scaled after applying log10 for logarithmic axes
        logCoords     -- index/indices of dimension(s) to be logarithmic, set to [] if no log coordinates
        basis         -- basis to normalize argument to logarithm (ie defines origin). List of same length as logCoords
        reverseCoords -- index/indices of dimension(s) to be reversed, set to [] if none to be reversed
        revCenter     -- center of reversal if reverseCoords is not empty. List of same length as logCoords
        replaceNaN    -- whether or not to replace the FillValue with NaNs
    OUTPUTS:
        output_nc     -- netCDF reader object with the file data as read
        transCoor     -- Calculator filter corresponding to the transformed coordinates
    """
    # outputDimensions must be in same sequence as in netCDF file, except time (e.g. ['pfull','lat','lon'] ). This is usually the "wrong" way round. Thus, we invert it here
    outputDimensions = ncDims[::-1]
    output_nc = NetCDFReader( FileName=[fileName] )

    if len(outputDimensions)>0 :
        outDims = '('+ outputDimensions[0]
        for dim in range(1,len(outputDimensions)):
            outDims = outDims + ', ' + outputDimensions[dim]
        outDims += ')'
        output_nc.Dimensions = outDims

    output_nc.SphericalCoordinates = 0
    output_nc.OutputType = 'Unstructured'
    output_nc.ReplaceFillValueWithNan = replaceNaN
    MakeSelectable()
    RenameSource(fileName,output_nc)

    transCoor = TransformCoords(src=output_nc,aspectRatios=aspectRatios,logCoords=logCoords,basis=basis,reverseCoords=reverseCoords,revCenter=revCenter)
    MakeSelectable()

    if len(logCoords)>0 :
        RenameSource('LogCoor',transCoor)
    else:
        RenameSource('TransCoor',transCoor)
    return output_nc,transCoor

######## convert 2D into 3D data using a variable as third dimension ##############

def Make3D( expandVar, expandDir='z', aspectRatios=[1,1,1], logCoords=[], basis=[], src=GetActiveSource() ):
    """Expand any 2D dataset into 3D with the values of a field.

        Make3D takes a 2D dataset, and adds a third dimension corresponding to a data field.

        INPUTS:
            expandVar    -- name of the variable to use as third dimension
            expandDir    -- direction in which to expand {'x','y','z'}. Make it negative for expanding in opposite direction: {'-x','-y','-z'}
            aspectRatios -- how to scale coordinates [xscale,yscale,zscale].
            logCoords    -- index/indices of dimension(s) to be logarithmic
            basis        -- basis to normalize argument to logarithm (ie defines origin). List of same length as logCoords
            src          -- source filter to attach to
        OUPUTS:
            make3d       -- a Calculator filter with the intermediate step of adding the variable into the coordinates.
            trans3d      -- a Calculator filter with the transformed 3D field
    """
    make3d = Calculator(src)
    sign = '+'
    if expandDir[0] == '-':
        sign = '-'
    if expandDir.lower()[-1] == 'x':
        make3d.Function = sign+'iHat*'+expandVar+' + jHat*coordsX + kHat*coordsY'
    elif expandDir.lower()[-1] == 'y':
        make3d.Function = 'iHat*coordsX '+sign+' jHat*'+expandVar+' + kHat*coordsY'
    elif expandDir.lower()[-1] == 'z':
        make3d.Function = 'iHat*coordsX + jHat*coordsY '+sign+' kHat*'+expandVar
    else:
        raise Exception("Make3D: expandDir has to be one of x,y,z, but is "+expandDir)
    make3d.CoordinateResults = 1

    trans3d = TransformCoords(src=make3d,aspectRatios=aspectRatios,logCoords=logCoords,basis=basis)
    return make3d,trans3d

######## some other usefull tools #################################################

# transform winds from SI to plot units
def CartWind2Sphere(src=GetActiveSource(), zonalComponentName='ucomp', meridionalComponentName='vcomp', secondsPerTimeStep=86400, verticalComponentName='none', ratios=[1,1,1], vertAsp=1 ):
    """Convert wind components from m/s to lat/timeStep, lon/timeStep, z/timeStep, and store it as vector W. This is, naturally, specific to spherical geometry, and assumes that coordsX = longitude [degrees], coordsY = latitude [degrees], and coordsZ = vertical coordinate. However, this is still only accurate if showing the winds on a flat lon x lat surface. For glyph vectors on the sphere, subsequently call Wind2SphericalVectors().

    Works with both pressure and height velocity, as long as vertAsp = [initial vertical range]/[present vertical range] is correct.
    INPUTS:
        src                     -- filter in pipeline to attach to
        zonalComponentName      -- name of zonal wind component in pipeline
        meridionalComponentName -- name of meridional wind component in pipeline
        secondsPerTimeStep      -- duration of time step in seconds: 86400 for daily
        verticalComponentName   -- name of vertical component, or 'none'
        ratios                  -- Corrections to actually plotted axes
        vertAsp                 -- factor for vertical unit conversion = [initial vertical range]/[present vertical range(transformed)]. Only needed if there is a vertical component
    OUTPUTS:
        Adds two Calculators to the pipeline:
        W     -- wind vector calculation
        normW -- magnitude of wind vector
        Adds two slices to the pipeline to remove division by zero close to poles:
        clipS -- remove south pole
        clipN -- remove north pole
    """
    W=Calculator(src)
    if verticalComponentName != 'none' :
        W.Function = '(' + \
        'iHat*'+zonalComponentName+'/(6.28*6.4e6*cos(coordsY/'+str(ratios[1])+'*'+strPi+'/180))*360 +' + \
        'jHat*'+meridionalComponentName+'/('+strPi+'*6.4e6)*180 +' + \
        'kHat*'+verticalComponentName+'/'+str(vertAsp) + \
        ')*'+str(secondsPerTimeStep)
    else:
        W.Function =  '(' + \
        'iHat*'+zonalComponentName+'/(6.28*6.4e6*cos(coordsY/'+str(ratios[1])+'*'+strPi+'/180))*360 +' + \
        'jHat*'+meridionalComponentName+'/('+strPi+'*6.4e6)*180' + \
        ')*'+str(secondsPerTimeStep)
    W.ResultArrayName = 'W'
    RenameSource('CartWind2Sphere',W)
    MakeSelectable(W)
    # add the magnitdue of the wind vector, i.e wind strength. nice to have for color, threshold, glyph filters later on
    norm = Calculator(W)
    norm.Function = 'mag(W)'
    norm.ResultArrayName = 'normW'
    RenameSource('normW',norm)
    MakeSelectable(norm)
    # conversion invloves a division by zero over the poles. to avoid large numbers, cut away anything higher than 80 degrees
    clipS = Clip(norm)
    clipS.ClipType = 'Plane'
    clipS.ClipType.Normal = [0.0, 1.0, 0.0]
    clipS.ClipType.Origin  = [0.0, -80.0*ratios[1], 0.0]
    try: # paraview v5.5+
        clipS.Invert = 0
    except:
        pass
    RenameSource('clipS',clipS)
    MakeSelectable(clipS)
    clipN = Clip(clipS)
    clipN.ClipType = 'Plane'
    clipN.ClipType.Normal = [0.0,-1.0, 0.0]
    clipN.ClipType.Origin  = [0.0, 80.0*ratios[1], 0.0]
    try: # paraview v5.5+
        clipN.Invert = 0
    except:
        pass
    RenameSource('clipN',clipN)
    MakeSelectable(clipN)
    return W,norm,clipS,clipN

def Wind2SphericalVectors(src=GetActiveSource(),vectorName='W'):
    """Perform the necessary vector algebra to represent wind components in units of lat/timeStep, lon/timeStep, z/timeStep on the sphere. These vectors are stored as vector V. Prior to this, you would probably want to run CartWind2Sphere() for the wind vectors to be in the appropriate units.

    You will probably want to run Cart2spherical() after this to put the whole thing into proper spherical geometry.
    INPUTS:
        src        -- filter in pipeline to attach to
        vectorName -- name of vector components in lat/timeStep, lon/timeStep, z/timeStep
    OUTPUTS:
        Adds five Calculators to the pipeline:
        P1    -- extract start position of vectors in flat geometry
        P2    -- extract end position of vectors in flat geometry
        Q1    -- start position of vectors in spherical geometry
        Q2    -- end position of vectors in spherical geometry
        V     -- final vector which can be used to drive, e.g., Glyph(), SurfaceLIC, Stream Lines, etc.
    """
    
    # flat vector start
    p1 = Calculator(registrationName='P1', Input=src)
    p1.ResultArrayName = 'P1'
    p1.Function = 'iHat*coordsX+jHat*coordsY+kHat*coordsZ'
    # flat vector stop
    p2 = Calculator(registrationName='P2', Input=p1)
    p2.ResultArrayName = 'P2'
    p2.Function = 'P1+'+vectorName
    # compute spherical vector start
    q1 = Calculator(registrationName='Q1', Input=p2)
    q1.ResultArrayName = 'Q1'
    q1.Function = 'iHat*(1.000+P1_Z)*cos(P1_Y*3.14159/180)*cos(P1_X*3.14159/180) + jHat*(1.000+P1_Z)*cos(P1_Y*3.14159/180)*sin(P1_X*3.14159/180) + kHat*(1.000+P1_Z)*sin(P1_Y*3.14159/180)'
    # compute spherical vector end
    q2 = Calculator(registrationName='Q2', Input=q1)
    q2.ResultArrayName = 'Q2'
    q2.Function = 'iHat*(1.000+P2_Z)*cos(P2_Y*3.14159/180)*cos(P2_X*3.14159/180) + jHat*(1.000+P2_Z)*cos(P2_Y*3.14159/180)*sin(P2_X*3.14159/180) + kHat*(1.000+P2_Z)*sin(P2_Y*3.14159/180)'
    # final vector is end point minus start point
    v = Calculator(registrationName='V', Input=q2)
    v.ResultArrayName = 'V'
    v.Function = 'Q2-Q1'
    return p1,p2,q1,q2,v




# extract the boundaries of a filter
def ExtractBounds(src=GetActiveSource()):
    """Return the axis extremities (bounds) of any source filter

        Inputs:
        src    - filter to extract bounds of
        Outputs:
        bounds - list of (xmin,xmax [,ymin,ymax [,zmin,zmax]])"""
    bounds = src.GetDataInformation().GetBounds()
    return bounds

## working with a spherical geometry: conversion functions
def Sphere2xyz(coords, lam=None, phi=None):
    """Compute (x,y,z) from coords=(r,lam,phi) or r,lam,phi, where lam=0 at the Equator, -90 <= lam <= 90 (latitude),
        and phi=0 along x-axis, 0 <= phi <= 360 (longitude)
        Also computes the normal along the radial direction (useful for placing and orienting the camera).

        INPUTS:
            coords - list of (radius,lambda,phi) or radius
            lam    - lambda (declination, latitude) if coords is radius
            phi    - phi (azimuth, longitude) if coords is radius
        OUTPUTS:
            xyzPos - list of corresponding (x,y,z)
            normal - list of (xn,yn,zn) along radial direction
    """
    from math import pi,sin,cos
    if isinstance(coords,list) or isinstance(coords,tuple):
    	if len(coords) == 3:
        	rr=coords[0];lam=coords[1];phi=coords[2]
    	else:
        	raise Exception("Sphere2xyz: coords has to be a list of length 3 (r,lambda,phi), or a scalar")
    else:
    	rr=coords
    xyzPos = [rr*cos(lam*pi/180)*cos(phi*pi/180),rr*cos(lam*pi/180)*sin(phi*pi/180),rr*sin(lam*pi/180)]
    rr=rr+1
    p1     = [rr*cos(lam*pi/180)*cos(phi*pi/180),rr*cos(lam*pi/180)*sin(phi*pi/180),rr*sin(lam*pi/180)]
    normal = []
    for i in range(len(p1)):
        normal.append(p1[i] - xyzPos[i])
    return xyzPos,normal
#
def xyz2Sphere(coords, y=None, z=None):
    """Compute (r,lam,phi) from coords=(x,y,z) or x,y,z, where lam=0 at the Equator, -90 <= lam <= 90 (latitude),
        and phi=0 along x-axis, 0 <= phi <= 360 (longitude)

        INPUTS:
            coords - list of (x,y,z) or x
            y      - y coordinate if coords is x
            z      - z coordinate if coords is x
        OUTPUTS:
            sphPos - list of corresponding (r,lam,phi)
    """
    from math import sqrt,pi,sin,cos,asin,atan
    if isinstance(coords,list) or isinstance(coords,tuple):
    	if len(coords) == 3:
        	x=coords[0];y=coords[1];z=coords[2]
    	else:
        	raise Exception("xyz2Sphere: coords has to be a list of length 3 (x,y,z), or a scalar")
    else:
    	x = coords
    r   = sqrt(x*x + y*y + z*z)
    if x > 0:
        phi = atan(y/x)
    elif x < 0:
        phi = pi + atan(y/x)
    elif x == 0 and y > 0:
        phi = 0.5*pi
    elif x == 0 and y < 0:
        phi = 1.5*pi
    lam = asin(z/r)
    return (r,lam*180/pi,phi*180/pi)


#
def SaveAnim(root,start=None,stop=None,stride=1,viewSize=None,verbose=1,transparent=False):
    """Save animation across all timesteps.
       Filename will be root.####.png.
       start and stop are assumed to be indices if integers, or 
        actual time else. All timesteps are used if None."""
    scene = GetAnimationScene()
    view = GetActiveViewOrCreate('RenderView')
    if viewSize is not None:
        view.ViewSize = viewSize
    if transparent:
        transparent = 1
    else:
        transparent = 0
    if start is None:
        start = scene.TimeKeeper.TimestepValues[0]
    if stop is None:
        stop = scene.TimeKeeper.TimestepValues[-1]
    if verbose > 1:
        nsteps = len(scene.TimeKeeper.TimestepValues)
        print('There is a total number of {0} time steps.'.format(nsteps))
    if isinstance(start,int):
        ms = start
    else:
        ms = scene.TimeKeeper.TimestepValues[:].index(start)
    if isinstance(stop,int):
        me = stop
    else:
        me = scene.TimeKeeper.TimestepValues[:].index(stop)
    if verbose > 1:
        print('Going from {0} to {1} with stride of {2}.'.format(ms,me,stride))
    for i,t in enumerate(scene.TimeKeeper.TimestepValues[ms:me:stride]):
        if verbose > 1:
            print('timestep ',t)
        scene.AnimationTime = t
        frameInd = '{0:04d}'.format(i)
        outFile = root+frameInd+'.png'
        SaveScreenshot(outFile,view=view,magnification=1,quality=100)
        if verbose > 0:
            print(outFile)


## some simple helper functions
#
def DeleteAll():
    """Delete all objects in the pipeline browser."""
    for src in GetSources().values():
        Delete(src)
#
def HideAll():
    """Make all objects in pipeline browser invisible."""
    for src in GetSources().values():
    	Hide(src)
#
def ShowAll():
    """Make all objects in pipeline browser visible."""
    for src in GetSources().values():
        Show(src)