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RMA2SERAPHIN
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RMA2SERAPHIN/RMA2SERAPHIN_3DRMA11_201911...

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# coding: utf-8
# In[64]:
import struct
import matplotlib.pyplot as plt
import math
from py_rmatools_v03 import rma
import re
from datetime import datetime, timedelta
import pandas as pd
import numpy as np
plt.rcParams.update({'figure.max_open_warning': 0})
# In[65]:
meshFilename = 'KMA003.rm1'
channelWidth = 100
RMAfilenames = ['KMA008']
#If RMA11
constNum = [1]
#If RMA11 3D
#Options = [4,8,1,'Max'] #Option available 'Max' , an integer correspond to the layer number to extract the results, if 2D use options = [1] - 'Percentile' (percentile only work for RMA11 FOR now)
Options = [9] #if we specified 8 layers in RMA10 then the bed layer is layer #9
percentiles = [0.5,0.8,0.9,0.95,1]
NodeLayersFile = 'NodeLayers003.txt' #the node layer file was created by getting the nodes number from the RMA Outfile (just run RMA11 for a few steps)
Nnodes = 6127 #Number of nodes (including mid side node) - thisn umber also correspond to the last node number in the nodelayers file
# In[66]:
def isElementOneD(nodelist1):
if len(nodelist1) == 3:
return True
return False
def isElementSquare(nodelist1):
if len(nodelist1) == 8:
return True
return False
def isElementTriangle(nodelist1):
if len(nodelist1) == 6:
return True
return False
def square2Triangle(ElementNum):
nodelist1 = ElementDict[ElementNum]
if isElementSquare(nodelist1):
ElementDict[ElementNum] = [nodelist1[0], nodelist1[1], nodelist1[7]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[1], nodelist1[2], nodelist1[3]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[1], nodelist1[3], nodelist1[7]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[3], nodelist1[4], nodelist1[5]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[3], nodelist1[5], nodelist1[7]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[5], nodelist1[6], nodelist1[7]]
def triangle2Triangles(ElementNum):
nodelist1 = ElementDict[ElementNum]
if isElementTriangle(nodelist1):
ElementDict[ElementNum] = [nodelist1[0], nodelist1[1], nodelist1[5]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[1], nodelist1[2], nodelist1[3]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[1], nodelist1[3], nodelist1[5]]
ElementList.append(max(ElementList) + 1)
ElementDict[ElementList[-1]]= [nodelist1[3], nodelist1[4], nodelist1[5]]
def oneD2triangle(ElementNum):
if isElementOneD(ElementDict[ElementNum]):
nAe = ElementDict[ElementNum][0] #nAe Node A existing
nBe = ElementDict[ElementNum][1]
if not nAe in node1Dduplicate: node1Dduplicate[nAe] = []
if not nBe in node1Dduplicate: node1Dduplicate[nBe] = []
xA = nodeDict[nAe][0]
xB = nodeDict[nBe][0]
yA = nodeDict[nAe][1]
yB = nodeDict[nBe][1]
normalVec = [-(yB - yA),(xB - xA)]
dist = math.sqrt(normalVec[0]**2 + normalVec[1]**2)
normalVec[0] = normalVec[0] / dist
normalVec[1] = normalVec[1] / dist
xA2 = xA + channelWidth * normalVec[0]
xB2 = xB + channelWidth * normalVec[0]
yA2 = yA + channelWidth * normalVec[1]
yB2 = yB + channelWidth * normalVec[1]
nA = max(NodeList) + 1
nB = max(NodeList) + 2
node1Dduplicate[nAe].append(nA)
node1Dduplicate[nBe].append(nB)
node2nodevalue[nA] = nAe
node2nodevalue[nB] = nBe
NodeList.append(nA)
NodeList.append(nB)
nodeDict[nA] = [xA2, yA2, -1.01]
nodeDict[nB] = [xB2, yB2, -1.01]
newEle = max(ElementList) + 1
ElementList .append(newEle)
ElementDict[ElementNum] = [nAe, nA, nBe]
ElementDict[newEle] = [nA, nB, nBe]
def RMA2toSerafin():
f = open('{}.slf'.format(RMAfilename), 'wb')
f.write(struct.pack(">l",80))
str='{0: >80}'.format('SERAFIN ')
f.write(str.encode('ascii'))
f.write(struct.pack(">l",80))
f.write(struct.pack(">l",8))
f.write(struct.pack(">l",len(constName)))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",8))
for c in constName:
f.write(struct.pack(">l",32))
str='{0: <32}'.format(c)
f.write(str.encode('ascii'))
f.write(struct.pack(">l",32))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",R.year))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",3))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)*3*4))
for el in ElementList:
for nd in ElementDict[el]:
f.write(struct.pack(">l",nodeOrdered[nd]))
f.write(struct.pack(">l",len(ElementList)*3*4))
f.write(struct.pack(">l",len(NodeList)))
for i in range(0,len(NodeList)):
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[0]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[1]))
f.write(struct.pack(">l",len(NodeList)*4))
while R.next():
f.write(struct.pack(">l",4))
f.write(struct.pack(">f",R.time * 3600))
f.write(struct.pack(">l",4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
f.write(struct.pack(">f",R.xvel[node2nodevalue[key]]))
else:
f.write(struct.pack(">f",R.xvel[key]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
f.write(struct.pack(">f",R.yvel[node2nodevalue[key]]))
else:
f.write(struct.pack(">f",R.yvel[key]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
f.write(struct.pack(">f",R.depth[node2nodevalue[key]]))
else:
f.write(struct.pack(">f",R.depth[key]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
f.write(struct.pack(">f",R.elevation[node2nodevalue[key]]))
else:
f.write(struct.pack(">f",R.elevation[key]))
f.write(struct.pack(">l",len(NodeList)*4))
f.close()
def RMA11toSerafin(option=1):
f = open('{}_{}.slf'.format(run,option), 'wb')
f.write(struct.pack(">l",80))
strtemp='{0: >80}'.format('SERAFIN ')
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",80))
f.write(struct.pack(">l",8))
f.write(struct.pack(">l",len(constName)))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",8))
for idx,c in enumerate(constName):
f.write(struct.pack(">l",32))
strtemp='{0: <32}'.format(str(idx)+c)
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",32))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",startDate.year))
f.write(struct.pack(">l",startDate.month))
f.write(struct.pack(">l",startDate.day))
f.write(struct.pack(">l",startDate.hour))
f.write(struct.pack(">l",startDate.minute))
f.write(struct.pack(">l",startDate.second))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",3))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)*3*4))
for el in ElementList:
for nd in ElementDict[el]:
f.write(struct.pack(">l",nodeOrdered[nd]))
f.write(struct.pack(">l",len(ElementList)*3*4))
f.write(struct.pack(">l",len(NodeList)))
for i in range(0,len(NodeList)):
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[0]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[1]))
f.write(struct.pack(">l",len(NodeList)*4))
while R.next():
#for i in range(3):
currentDate = datetime(R.year,1,1) + timedelta(hours = R.time)
timeCurrentStep = currentDate - startDate
f.write(struct.pack(">l",4))
f.write(struct.pack(">f",timeCurrentStep.total_seconds()))
f.write(struct.pack(">l",4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
writeConst('X-VEL',key,f)
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
writeConst('Y-VEL',key,f)
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
writeConst('DEPTH',key,f)
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
writeConst('FREE SURFACE',key,f)
f.write(struct.pack(">l",len(NodeList)*4))
for c in constNum:
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
writeConst(c,key,f)
f.write(struct.pack(">l",len(NodeList)*4))
f.close()
def RMA10toSerafin(option=1):
f = open('{}_{}.slf'.format(run,option), 'wb')
f.write(struct.pack(">l",80))
strtemp='{0: >80}'.format('SERAFIN ')
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",80))
f.write(struct.pack(">l",8))
f.write(struct.pack(">l",len(constName)))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",8))
for idx,c in enumerate(constName):
f.write(struct.pack(">l",32))
strtemp='{0: <32}'.format(str(idx)+c)
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",32))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",startDate.year))
f.write(struct.pack(">l",startDate.month))
f.write(struct.pack(">l",startDate.day))
f.write(struct.pack(">l",startDate.hour))
f.write(struct.pack(">l",startDate.minute))
f.write(struct.pack(">l",startDate.second))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",3))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)*3*4))
for el in ElementList:
for nd in ElementDict[el]:
f.write(struct.pack(">l",nodeOrdered[nd]))
f.write(struct.pack(">l",len(ElementList)*3*4))
f.write(struct.pack(">l",len(NodeList)))
for i in range(0,len(NodeList)):
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[0]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[1]))
f.write(struct.pack(">l",len(NodeList)*4))
while R.next():
#for i in range(3):
currentDate = datetime(R.year,1,1) + timedelta(hours = R.time)
timeCurrentStep = currentDate - startDate
f.write(struct.pack(">l",4))
f.write(struct.pack(">f",timeCurrentStep.total_seconds()))
f.write(struct.pack(">l",4))
# f.write(struct.pack(">l",len(NodeList)*4))
# for key, value in nodeDict.items():
# writeConst('X-VEL',key,f)
# f.write(struct.pack(">l",len(NodeList)*4))
for c in constName:
f.write(struct.pack(">l",len(NodeList)*4))
data = [None] * len(nodeDict)
idx = 0
for key, value in nodeDict.items():
data[idx] = writeConst(c,key)
idx += 1
f.write(b''.join(data))
f.write(struct.pack(">l",len(NodeList)*4))
f.close()
def writeConst(param,key):
#get the surface node number
# ['X-VEL','Y-VEL','DEPTH','FREE SURFACE','Constituent 1'......]
if param == 'X-VEL':
tempR = R.xvel
elif param == 'Y-VEL':
tempR = R.yvel
elif param == 'Z-VEL':
tempR = R.zvel
elif param == 'DEPTH':
tempR = R.depth
elif param == 'FREE SURFACE':
tempR = R.elevation
elif param == 'TEMPERATURE':
tempR = R.temperature
elif param == 'SALINITY':
tempR = R.salinity
elif param == 'SSED':
tempR = R.sussed
else:
tempR = R.constit[c]
if key in node2nodevalue.keys():
key = node2nodevalue[key]
#based on the surface node number and option selected calculate the value
if option == 'Max':
tempArr = []
for n in nodelayer[key]:
tempArr.append(tempR[n])
tempVal1 = max(tempArr)
elif isinstance(option, int):
if key in cornerNodes:
temppos = (option - 1 ) * 2
else:
temppos = option
temppos2 = min([temppos,len(nodelayer[key])-1])
tempVal1 = tempR[nodelayer[key][temppos2]]
else:
tempVal1 = tempR[key]
#save the value in the selaphin file
#f.write(struct.pack(">f",tempVal1))
return struct.pack(">f",tempVal1)
def writePCTL(c,pctl):
f = open('{}_{}_{}.slf'.format(run,c,option), 'wb')
f.write(struct.pack(">l",80))
strtemp='{0: >80}'.format('SERAFIN ')
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",80))
f.write(struct.pack(">l",8))
f.write(struct.pack(">l",len(pctl)))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",8))
for idx,p in enumerate(pctl):
f.write(struct.pack(">l",32))
strtemp='{0: <32}'.format(str(idx)+ 'pct ' + str(p))
f.write(strtemp.encode('ascii'))
f.write(struct.pack(">l",32))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",40))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",startDate.year))
f.write(struct.pack(">l",startDate.month))
f.write(struct.pack(">l",startDate.day))
f.write(struct.pack(">l",startDate.hour))
f.write(struct.pack(">l",startDate.minute))
f.write(struct.pack(">l",startDate.second))
f.write(struct.pack(">l",24))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",3))
f.write(struct.pack(">l",1))
f.write(struct.pack(">l",16))
f.write(struct.pack(">l",len(ElementList)*3*4))
for el in ElementList:
for nd in ElementDict[el]:
f.write(struct.pack(">l",nodeOrdered[nd]))
f.write(struct.pack(">l",len(ElementList)*3*4))
f.write(struct.pack(">l",len(NodeList)))
for i in range(0,len(NodeList)):
f.write(struct.pack(">l",0))
f.write(struct.pack(">l",len(NodeList)))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[0]))
f.write(struct.pack(">l",len(NodeList)*4))
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
f.write(struct.pack(">f",value[1]))
f.write(struct.pack(">l",len(NodeList)*4))
columnName = [node2nodevalue[key] if key in node2nodevalue.keys() else key for key, value in nodeDict.items()]
global dfAll
dfAll = {}
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
key = node2nodevalue[key]
dfAll[key] = np.array([])
cpt = 0
currentDate = datetime(R.year,1,1) + timedelta(hours = R.time)
timeCurrentStep = currentDate - startDate
f.write(struct.pack(">l",4))
f.write(struct.pack(">f",timeCurrentStep.total_seconds()))
f.write(struct.pack(">l",4))
while R.next():
tempR = R.constit[c]
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
key = node2nodevalue[key]
tempArr = []
for n in nodelayer[key]:
tempArr.append(tempR[n])
tempVal1 = max(tempArr)
dfAll[key] = np.append(dfAll[key],tempVal1)
cpt = cpt + 1
for p in pctl:
f.write(struct.pack(">l",len(NodeList)*4))
for key, value in nodeDict.items():
if key in node2nodevalue.keys():
key = node2nodevalue[key]
f.write(struct.pack(">f",np.quantile(dfAll[key],p)))
f.write(struct.pack(">l",len(NodeList)*4))
def readNodeLayers(fname,Nnodes):
fn = open(fname)
lines = fn.readlines()
surfaceNode = int(lines[0])
nodelayer[surfaceNode] = []
for l in lines:
l = int(l)
if (l != surfaceNode) & (l < Nnodes + 1):
surfaceNode = l
nodelayer[surfaceNode] = []
nodelayer[surfaceNode].append(l)
# In[67]:
#Read mesh file and extract node (except mid node) and elements - plus convert 1D element to 2D for vizualisation
nodelayer = {}
midSideNodes = []
cornerNodes = []
NodeList = []
ElementList = []
ElementDict = {}
nodeDict = {}
node1Dduplicate = {} #Original Number: List of Duplicates
node2nodevalue = {} #link between the node number and the node value to use
#(e.g. if node 10 is a 1D node: 10 is not duplicate so {1:1},
#but node 2050 (duplicate of 10) (1D to 2D) the value of the duplicated
#node will be the same as the original so we might have {2050: 10})
with open(meshFilename) as f:
line = f.readline()
line = f.readline()
line = f.readline()
line = f.readline()
cpt = 1
while line and line != ' 9999\n':
#temp = line.split()
temp = re.findall('.....',line)
ElementDict[int(temp[0])] = [int(temp[i]) for i in range(1,9) if int(temp[i]) != 0 and int(temp[9]) < 100]
for idx, n in enumerate(ElementDict[int(temp[0])]):
if idx%2 == 0:
cornerNodes.append(n)
else:
midSideNodes.append(n)
ElementList.append(int(temp[0]))
line = f.readline()
for key, value in ElementDict.items():
NodeList.extend(value)
NodeList = list(set(NodeList))
cornerNodes = list(set(cornerNodes))
midSideNodes = list(set(midSideNodes))
line = f.readline()
while line and line != ' 9999\n':
formatFix = (10,16,20,14,10,10)
temp = []
for form in formatFix:
temp.append(line[:form])
line = line[form:]
#line.split()
if int(temp[0]) in NodeList:
nodeDict[int(temp[0])] = [float(temp[1]),float(temp[2]),float(temp[3])]
line = f.readline()
print('Processing triangles')
ElementList2 = ElementList[:]
for e in ElementList2:
print(e)
if isElementTriangle(ElementDict[e]):
triangle2Triangles(e)
elif isElementOneD(ElementDict[e]):
oneD2triangle(e)
else:
square2Triangle(e)
for key in list(ElementDict): #Remove Special Element 902.....
if len(ElementDict[key]) != 3:
print(key, ElementDict[key])
ElementDict.pop(key)
ElementList.remove(key)
nodeOrdered = {}
cpt = 1
for key, value in nodeDict.items():
nodeOrdered[key] = cpt
cpt +=1
# # Open and Read First Step of the RMA File and Save a Serafin
# In[72]:
for run in RMAfilenames:
for option in Options:
RMAfilename = '{}/{}'.format(run,run)
R=rma()
R.open(RMAfilename)
R.next()
startDate = datetime(R.year,1,1) + timedelta(hours = R.time)
if R.type==b'RMA11 ':
constName = []
readNodeLayers(NodeLayersFile,Nnodes)
constName = ['X-VEL','Y-VEL','DEPTH','FREE SURFACE']
for c in constNum:
constName.append(R.constit_name[c].decode("utf-8"))
print(c)
if option == 'Percentile':
for c in constNum:
writePCTL(c,percentiles)
else:
RMA11toSerafin(option)
if R.type=='RMA10 ':
constName = []
readNodeLayers(NodeLayersFile,Nnodes)
constName = ['X-VEL','Y-VEL','Z-VEL','FREE SURFACE','SALINITY','TEMPERATURE']
if option == 'Percentile':
for c in constNum:
writePCTL(c,percentiles)
else:
RMA10toSerafin(option)
if R.type==b'RMA2 ':
constName = ['X-VEL','Y-VEL','DEPTH','FREE SURFACE']
RMA2toSerafin()
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