(bar2vtk) Allow arbitrary read/write values

[jrwrigh]

Allow for reading in arbitrary binary files with arbitrary ordering of data. Namely for SST velbar files, which include the TKE and Omega in them.

Allow for explicitly declaring the order of the components of a binary array by a comma-separated string, and have automatic treatment of those values.

Standard processed values:

String	Value
u, v, w	(Mean) Velocity components
p	(Mean) pressure
uu, vv, ww, uv, uw, vw	(Mean) Velocity product (to calculate Reynolds stress by <u'u'> = <uu> - <u><u> )

Any other values parsed will simply be passed to the vtm file.

Examples:

Example	String
Standard velbar file	'u,v,w,p'
Standard stsbar file	'uu,vv,ww,uv,uw,vw'
SST velbar file	'u,v,w,p,k,omega'

[jrwrigh]

Psuedocode/snippets:

def parseArbitraryInput(input: str):
    collist = input.split(',')
    velmap = ['u', 'v', 'w']
    reystrmap = ['uu', 'vv', 'ww', 'uv', 'uw', 'vw']
    velindx =  [-1]*3
    reystrindx = [-1]*6
    other = {}
	for i, col in enumerate(collist):
        if col in velmap:
            velindx[velmap.index(col)] = i
        elif col in reystrmap:
            reystrindx[reystrmap.index(col)] = i
        else:
            other[col] = i
    return velindx, reystrindx, other

Assume we have two lists: inputs and files, each entry of which corresponds to the others (so inputs[0] is the input string for files[0]). This would come out of the CLI parser.

# npnts defined somewhere else
data = {}
for input, file in zip(inputs, files):
    velindx, resystrindx, other = parseAribtraryInputs(input)
	ncols = len(velindx) + len(reystrindx) + len(other)
    rawdata = readBinaryArray(file, ncols)
    
    if not all([-1 == n for n in velindx]):
		if not 'Velocity' in data.keys(): data['Velocity'] = np.zeros((npnts,3))
		for i, idx in enumerate(velindx):
			if not idx == -1:
				data['Velocity'][i,:] = rawdata[idx,:]
	# Repeat for reynolds stress
    if other:
		for label, idx in other.items():
			data[label] = rawdata[idx,:]

data is now a dictionary of the "Velocity", "ReynoldsStress", and other random labels.