def __init__(self, fileName):
#Read the file containg probe data and store it in this object
CompoProfile.__init__(self)
self.pltMark = 'o'
#open the csv file
try:
grtFile = open(fileName, 'r')
except:
print("No csv file found at location:")
print(fileName)
return
grtdf = pd.read_csv(grtFile)
self.x = list(grtdf['x (mm)'])
for i in range(len(CMPNT)):
self.cmpnts[i] = list(grtdf[CMPNT[i]])
def splitTrav(self, xPos, selectLeft):
#Method for splitting the traverse into two halves at the inputted xPos
#Assumes xpos will never exactly equal to an x position on the traverse
#The two halves are CompoProfile objects with the same data of their respective halves of this Traverse object
#They will be stored in the travSplit array so that they can be ambiguously referenced.
#They will contain a little less info but maintain most of the core stuff
count = 0
#Finds the index of the datapoint to the right of the selected x
while (self.x[count] < xPos):
count += 1
xRightIndex = count
xLeftIndex = count - 1
#initialize travSplit array to hold the two halves and the two sides of the traverse
self.travSplit = []
rightTrav = CompoProfile()
leftTrav = CompoProfile()
rightTrav.pltMark = 'o'
leftTrav.pltMark = 'o'
leftTrav.pltColour = 'blue' #So it can be differentiated on the plot
#Build the contained arrays
#First calculate the value at 0 using linear interpolation
#This allows for modelling from 0
rightTrav.x.append(0)
leftTrav.x.append(0)
for i in range(len(GRT_CMPNT)):
#Append the composition at 0 to both left and right traverse since they should be the same
zeroVal = self.interpCompoAtX(xPos, GRT_CMPNT[i].cation)
rightTrav.cmpnts[i].append(zeroVal)
leftTrav.cmpnts[i].append(zeroVal)
for i in range(xRightIndex, len(self.x)):
rightTrav.x.append(self.x[i] - xPos)
for j in range(len(GRT_CMPNT)):
rightTrav.cmpnts[j].append(self.cmpnts[j][i])
#Flips the left Traverse
for i in range(xLeftIndex, -1, -1):
leftTrav.x.append(xPos - self.x[i])
for j in range(len(GRT_CMPNT)):
leftTrav.cmpnts[j].append(self.cmpnts[j][i])
#Add the two traverses to travSplit
if len(rightTrav.x) > 0:
self.travSplit.append(rightTrav)
if not selectLeft:
return rightTrav
if len(leftTrav.x) > 0:
self.travSplit.append(leftTrav)
if selectLeft:
return leftTrav
def plotAll(self, pltIn):
#Method to plot all components on one plot
#Assumes that the Fe component is much higher than the rest, plots it on seperate axis
colours = ['green', 'blue', 'orange', 'red']
symbols = ['o', '^', 's', 'P']
pltAlm = pltIn.twinx()
self.travPlot = pltIn #Saves the plot to the object
#Loop for plotting
for i in range(len(CMPNT)):
self.pltColour = colours[i]
self.pltMark = symbols[i]
if (CMPNT[i] == "Fe"):
CompoProfile.plotCompo(self, CMPNT[i], pltAlm, 7)
else:
CompoProfile.plotCompo(self, CMPNT[i], pltIn, 7)
pltIn.set_xlabel("x (mm)")
pltIn.set_ylabel("X (Ca,Mn,Mg)")
#Uncomment these lines if you want everything on the same scale
#pltIn.set_ylim(0,0.4)
#pltAlm.set_ylim(0.45,0.85)
pltAlm.set_ylabel("X (Fe)")
pltIn.legend(fontsize=14, loc='upper left')
pltAlm.legend(fontsize=14, loc='upper right')
#This is to set up the stuff for splitting the plot in half, assuming that you input a full traverse instead of a half traverse
self.cid = pltIn.figure.canvas.mpl_connect('button_press_event',
self.travClick)
self.splitLine = pltIn.plot([0], [0]) #create an empty line
self.splitTrav(
self.x[0] - 1
) #Sets the baseline to leftTrav is empty and rightTrav = this. This is basically if you want to input just a half traverse, however it assumes that it is the right half
def splitTrav(self, xPos):
#Method for splitting the traverse into two halves at the inputted xPos
#Assumes xpos will never exactly equal to an x position on the traverse
#The two halves are CompoProfile objects with the same data of their respective halves of this Traverse object
#They will be stored in the travSplit array so that they can be ambiguously referenced.
#They will contain a little less info but maintain most of the core stuff
count = 0
#Finds the index of the datapoint to the right of the selected x
while (self.x[count] < xPos):
count += 1
xRightIndex = count
xLeftIndex = count - 1
#initialize travSplit array to hold the two halves and the two sides of the traverse
self.travSplit = []
rightTrav = CompoProfile()
leftTrav = CompoProfile()
rightTrav.pltMark = 'o'
leftTrav.pltMark = 'o'
leftTrav.pltColour = 'blue' #So it can be differentiated on the plot
#Build the contained arrays
for i in range(xRightIndex, len(self.x)):
rightTrav.x.append(self.x[i] - xPos)
for j in range(len(CMPNT)):
rightTrav.cmpnts[j].append(self.cmpnts[j][i])
#Flips the left Traverse
for i in range(xLeftIndex, -1, -1):
leftTrav.x.append(xPos - self.x[i])
for j in range(len(CMPNT)):
leftTrav.cmpnts[j].append(self.cmpnts[j][i])
#Add the two traverses to travSplit
if len(rightTrav.x) > 0:
self.travSplit.append(rightTrav)
if len(leftTrav.x) > 0:
self.travSplit.append(leftTrav)
def __init__(self, dirIn, gen, trial):
#Constructor, builds the data arrays defined in CompoProfile from the garnet_gen file
#Also defines the PTt path from PTt-path.txt
CompoProfile.__init__(self)
#Plot parameters
self.pltLine = '-'
self.pltColour = 'red'
self.trial = -1 #Easy way to check if initialized
self.gen = -1 #to use for checking if the gen exists for this trial
#self.profPlots = []
trialDir = 'Trial-' + '{:04d}'.format(trial)
if os.name == 'nt': #PC
slash = "\\"
else: #Mac
slash = "/"
#File paths for the PTt path and garnet composition
pathDir = dirIn + slash + trialDir + slash + PATH_FILE_NAME
grtDir = dirIn + slash + trialDir + slash + GRT_FILE_PREF + '{:03d}'.format(
gen) + 'a.txt'
try:
pathFile = open(pathDir, 'r')
except:
print("PTt-path.txt for trial: " + str(trial) +
" not found at location:")
print(pathDir)
return
self.trial = trial
try:
grtFile = open(grtDir, 'r')
except:
print("Garnet generation: " + str(gen) + " not found in trial: " +
str(trial))
print(
"Please select different generation if you wish to include this trial"
)
return
#grtFile.close()
self.gen = gen
self.pressure = []
self.temperature = []
self.time = []
line = pathFile.readline() #remove header
line = pathFile.readline()
#Read the path file to the end
while (len(line) > 0):
items = [value.strip() for value in line.split()]
self.temperature.append(float(items[TEMP_COL]))
self.pressure.append(float(items[PRES_COL]))
self.time.append(float(items[TIM_COL]))
line = pathFile.readline()
pathFile.close()
#Read the garnet file, need to specifically take the last growth period, starts from the bottom and moves up
#Header names are identical to output files from theriag, do not change these unless you change the theriag output as well
grtdf = pd.read_csv(grtFile)
rowCount = grtdf.shape[0]
shells = grtdf['shell ']
xCol = grtdf['node(cm) ']
#Build array of arrays in correpsonding order of CMPNT
tgCmpnt = []
for i in range(len(CMPNT)):
head = 'x(' + CMPNT[i] + ') '
tgCmpnt.append(grtdf[head])
row = rowCount - 1
#Will add the values from the corresponding columns then reverse them
self.x.append(xCol[row] * 10 - H_ADJUST)
for i in range(len(CMPNT)):
self.cmpnts[i].append(tgCmpnt[i][row])
row -= 1
#loop from end of the file, counting down the shells, stops when the shell
#number increases again, indicating an earlier stage of growth
while (shells[row] < shells[row + 1]):
self.x.append(xCol[row] * 10 - H_ADJUST)
for i in range(len(CMPNT)):
self.cmpnts[i].append(tgCmpnt[i][row])
#print(shells[row])
row -= 1
self.x.reverse()
for i in range(len(CMPNT)):
self.cmpnts[i].reverse()
def plotAll(self, pltIn):
#Method to plot all components on one plot
#Assumes that the Fe component is much higher than the rest, plots it on seperate axis
colours = ['green', 'blue', 'orange', 'red']
symbols = ['o', '^', 's', 'P']
pltAlm = pltIn.twinx()
self.travPlot = pltIn #Saves the plot to the object
#Loop for plotting
for i in range(len(GRT_CMPNT)):
self.pltColour = colours[i]
self.pltMark = symbols[i]
if (GRT_CMPNT[i] == ALM):
CompoProfile.plotCompo(self, GRT_CMPNT[i].cation, pltAlm, 7)
else:
CompoProfile.plotCompo(self, GRT_CMPNT[i].cation, pltIn, 7)
pltIn.set_xlabel("Distance (mm)", fontsize=24)
pltIn.set_ylabel("X (Ca,Mn,Mg)", fontsize=24)
#Uncomment these lines if you want everything on the same scale
pltIn.set_ylim(0, 0.4)
pltAlm.set_ylim(0.4, 0.9)
pltAlm.set_ylabel("X (Fe)", fontsize=24, rotation=-90)
pltIn.legend(loc='upper left')
pltAlm.legend(loc='upper right')
pltIn.xaxis.set_tick_params(which='major',
size=10,
width=2,
direction='in',
top='on')
pltIn.xaxis.set_tick_params(which='minor',
size=7,
width=2,
direction='in',
top='on')
pltIn.yaxis.set_tick_params(which='major',
size=10,
width=2,
direction='in',
right=False)
pltIn.yaxis.set_tick_params(which='minor',
size=7,
width=2,
direction='in',
right=False)
pltAlm.xaxis.set_tick_params(which='major',
size=10,
width=2,
direction='in',
top='on')
pltAlm.xaxis.set_tick_params(which='minor',
size=7,
width=2,
direction='in',
top='on')
pltAlm.yaxis.set_tick_params(which='major',
size=10,
width=2,
direction='in',
right=True)
pltAlm.yaxis.set_tick_params(which='minor',
size=7,
width=2,
direction='in',
right=True)
pltIn.xaxis.set_major_locator(mpl.ticker.MultipleLocator(1))
pltIn.xaxis.set_minor_locator(mpl.ticker.MultipleLocator(0.2))
pltIn.yaxis.set_major_locator(mpl.ticker.MultipleLocator(0.1))
pltIn.yaxis.set_minor_locator(mpl.ticker.MultipleLocator(0.02))
pltAlm.xaxis.set_major_locator(mpl.ticker.MultipleLocator(1))
pltAlm.xaxis.set_minor_locator(mpl.ticker.MultipleLocator(0.2))
pltAlm.yaxis.set_major_locator(mpl.ticker.MultipleLocator(0.1))
pltAlm.yaxis.set_minor_locator(mpl.ticker.MultipleLocator(0.02))
#This is to set up the stuff for splitting the plot in half, assuming that you input a full traverse instead of a half traverse
self.cid = pltIn.figure.canvas.mpl_connect('button_press_event',
self.travClick)
self.splitLine = pltIn.plot([0], [0]) #create an empty line
self.selectedTrav = self.splitTrav(
self.x[0] - 1, False
) #Sets the baseline to leftTrav is empty and rightTrav = this. This is basically if you want to input just a half traverse, however it assumes that it is the right half