def readFromFile_CoordsXYZ(FN, forceRead=False): # Sanity check filename: if not forceRead: doRegexMatch(FN,names.pixelCoordsFNRE) assert (fileExists(FN)) # Read (x,y,z) coordinate: #dataRegex = myRE.compile(myRE.withinSpaces(myRE.floatREx3)) dataRegex = myRE.compile(myRE.floatREx3) coords = np.fromregex(FN,dataRegex,dtype='f') # Return the array return coords
def readFromFile_CoordsAB_header(FN, forceRead=False): # Sanity check filename: if not forceRead: doRegexMatch(FN,names.pixelCoords2DFNRE) assert (fileExists(FN)) # Read header from coordinates file: coordsFile = open(FN) coordsFile_row1 = coordsFile.readline() # "a= [%f %f %f]" line coordsFile_row2 = coordsFile.readline() # "b= [%f %f %f]" line coordsFile_row3 = coordsFile.readline() # "%i %i" line, yielding (Na, Nb) coordsFile.close() # Analyse the read Strings: row1_RE = "a= \[" + myRE.withinSpaces(myRE.floatREx3) + "\]" row1_RO = myRE.compile(row1_RE) span_a_str = myRE.getMatchingGroups(coordsFile_row1, row1_RO) row2_RE = "b= \[" + myRE.withinSpaces(myRE.floatREx3) + "\]" row2_RO = myRE.compile(row2_RE) span_b_str = myRE.getMatchingGroups(coordsFile_row2, row2_RO) row3_RO = myRE.compile(myRE.group(myRE.intRE) + " " + myRE.group(myRE.intRE)) npix_str = myRE.getMatchingGroups(coordsFile_row3, row3_RO) #print(span_a) #print(span_b) #print(npix) # Convert str tuple to ints/floats tuple: npix=() for item in npix_str: npix += (int(item),) span_a=() for item in span_a_str: span_a += (float(item),) span_b=() for item in span_b_str: span_b += (float(item),) # Done! return (npix, (span_a,span_b))
def getResultDirs(mainDir):
# Sanity:
# TODO
# List content of mainDir:
content = sortArray(os.listdir(mainDir))
#print("content = " + str(content))
innerResDNs = myRE.getMatchingItems(content, myRE.compile(names.resInnerDNRE))
if (len(innerResDNs) > 0):
# We must have inner result directories
# so return an array of them
# First prepend mainDir:
for i, item in enumerate(innerResDNs):
innerResDNs[i] = os.path.join(mainDir, item)
return innerResDNs
else:
# There are no inner result directories
# so just return the main one
return [mainDir]
#! /usr/bin/env python3
import helpers.nameConventions as names
import helpers.regex as myRE
if __name__ == '__main__':
print("Now testing writer:")
print(names.resDN())
print(names.resDN("a"))
print(names.resInnerDN("2"))
print(names.resInnerDN("73"))
try:
print(names.resInnerDN("a"))
except:
print("Inner result directory error with \"a\".")
print("Now testing reader:")
print(myRE.getMatch(names.resDN(), myRE.compile(names.resDNRE)))
print(myRE.getMatch(names.resDN("a"), myRE.compile(names.resDNRE)))
print(
myRE.getMatch(names.resInnerDN("2"), myRE.compile(names.resInnerDNRE)))
# EOF
def natural_keys(text):
try:
return atof( myRE.getMatchingGroups(text, myRE.compile(r"[^\d]*" + myRE.group(myRE.floatRE)))[0] )
except:
return float("inf")
"Required arguments for the chosen speckle contrast function (if any). "
+ "Separate the parameters with a semicolon (e.g., --args \"a;b\").")
parser.add_option("-v",
action="store_true",
dest="verbose",
default=False,
help="verbose [default: %default]")
(opt, args) = parser.parse_args()
myPrint.Printer.verbose = opt.verbose
# Pre-parse arguments
(SC_args, SC_kwargs) = RTS.multiArgStringToArgs(opt.SC_args)
# Detect whether input is an intensity file or a directory:
if myRE.doesItemMatch(os.path.basename(opt.inFDN),
myRE.compile(names.intensityFNRE)):
# Then input is an intensity filename
# Read input:
(data, time, index) = optoFluidsIO.readFromFile_Intensity(opt.inFDN)
# Compute and output:
print(computeSpeckleContrast(data, opt.SC_func, *SC_args, **SC_kwargs))
else:
# Else input is not an intensity filename. Check whether it is a result directory.
# Get multiple result directories (if any):
resultDNs = optoFluidsIO.getResultDirs(opt.inFDN)
# Compute:
SCarray = []
for resDN in resultDNs:
# TODO: How to select the appropriate intensity file? CLI?
try: # Prioritize blurred:
argument = resDN + '/2D/blurred/Intensity2D_t0.0'