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Trace.py
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from ImportDependence import *
from CustomClass import *
class Trace(AppForm):
xticks = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
30, 31, 32, 33, 34, 35, 36, 37]
xticklabels = [u'',u'Cs', u'Tl', u'Rb', u'Ba', u'W', u'Th', u'U', u'Nb', u'Ta', u'K', u'La', u'Ce', u'Pb', u'Pr', u'Mo',
u'Sr', u'P', u'Nd', u'F', u'Sm', u'Zr', u'Hf', u'Eu', u'Sn', u'Sb', u'Ti', u'Gd', u'Tb', u'Dy',
u'Li',
u'Y', u'Ho', u'Er', u'Tm', u'Yb', u'Lu']
itemstocheck = ['Cs', 'Tl', 'Rb', 'Ba', 'W', 'Th', '', 'Nb', 'Ta', 'K', 'La', 'Ce', 'Pb', 'Pr', 'Mo',
'Sr', 'P', 'Nd', 'F', 'Sm', 'Zr', 'Hf', 'E', 'Sn', 'Sb', 'Ti', 'Gd', 'Tb', 'Dy',
'Li',
'Y', 'Ho', 'Er', 'Tm', 'Yb', 'Lu']
StandardsName = ['PM','OIB', 'EMORB', 'C1', 'NMORB','UCC_Rudnick & Gao2003']
reference = 'Reference: Sun, S. S., and Mcdonough, W. F., 1989, UCC_Rudnick & Gao2003'
NameChosen = 'PM'
Standards = {
'PM': {'Cs': 0.032, 'Tl': 0.005, 'Rb': 0.635, 'Ba': 6.989, 'W': 0.02, 'Th': 0.085, 'U': 0.021, 'Nb': 0.713,
'Ta': 0.041, 'K': 250, 'La': 0.687, 'Ce': 1.775, 'Pb': 0.185, 'Pr': 0.276, 'Mo': 0.063, 'Sr': 21.1,
'P': 95, 'Nd': 1.354, 'F': 26, 'Sm': 0.444, 'Zr': 11.2, 'Hf': 0.309, 'Eu': 0.168, 'Sn': 0.17,
'Sb': 0.005, 'Ti': 1300, 'Gd': 0.596, 'Tb': 0.108, 'Dy': 0.736, 'Li': 1.6, 'Y': 4.55, 'Ho': 0.164,
'Er': 0.48, 'Tm': 0.074, 'Yb': 0.493, 'Lu': 0.074},
'OIB': {'Cs': 0.387, 'Tl': 0.077, 'Rb': 31, 'Ba': 350, 'W': 0.56, 'Th': 4, 'U': 1.02, 'Nb': 48, 'Ta': 2.7,
'K': 12000, 'La': 36, 'Ce': 80, 'Pb': 3.2, 'Pr': 9.7, 'Mo': 2.4, 'Sr': 660, 'P': 2700, 'Nd': 38.5,
'F': 1150, 'Sm': 10, 'Zr': 280, 'Hf': 7.8, 'Eu': 3, 'Sn': 2.7, 'Sb': 0.03, 'Ti': 17200, 'Gd': 7.62,
'Tb': 1.05, 'Dy': 5.6, 'Li': 5.6, 'Y': 29, 'Ho': 1.06, 'Er': 2.62, 'Tm': 0.35, 'Yb': 2.16, 'Lu': 0.3},
'EMORB': {'Cs': 0.063, 'Tl': 0.013, 'Rb': 5.04, 'Ba': 57, 'W': 0.092, 'Th': 0.6, 'U': 0.18, 'Nb': 8.3,
'Ta': 0.47, 'K': 2100, 'La': 6.3, 'Ce': 15, 'Pb': 0.6, 'Pr': 2.05, 'Mo': 0.47, 'Sr': 155, 'P': 620,
'Nd': 9, 'F': 250, 'Sm': 2.6, 'Zr': 73, 'Hf': 2.03, 'Eu': 0.91, 'Sn': 0.8, 'Sb': 0.01, 'Ti': 6000,
'Gd': 2.97, 'Tb': 0.53, 'Dy': 3.55, 'Li': 3.5, 'Y': 22, 'Ho': 0.79, 'Er': 2.31, 'Tm': 0.356,
'Yb': 2.36, 'Lu': 0.354},
'C1': {'Cs': 0.188, 'Tl': 0.14, 'Rb': 2.32, 'Ba': 2.41, 'W': 0.095, 'Th': 0.029, 'U': 0.008, 'Nb': 0.246,
'Ta': 0.014, 'K': 545, 'La': 0.236, 'Ce': 0.612, 'Pb': 2.47, 'Pr': 0.095, 'Mo': 0.92, 'Sr': 7.26,
'P': 1220, 'Nd': 0.467, 'F': 60.7, 'Sm': 0.153, 'Zr': 3.87, 'Hf': 0.1066, 'Eu': 0.058, 'Sn': 1.72,
'Sb': 0.16, 'Ti': 445, 'Gd': 0.2055, 'Tb': 0.0364, 'Dy': 0.254, 'Li': 1.57, 'Y': 1.57, 'Ho': 0.0566,
'Er': 0.1655, 'Tm': 0.0255, 'Yb': 0.17, 'Lu': 0.0254},
'NMORB': {'Cs': 0.007, 'Tl': 0.0014, 'Rb': 0.56, 'Ba': 6.3, 'W': 0.01, 'Th': 0.12, 'U': 0.047, 'Nb': 2.33,
'Ta': 0.132, 'K': 600, 'La': 2.5, 'Ce': 7.5, 'Pb': 0.3, 'Pr': 1.32, 'Mo': 0.31, 'Sr': 90, 'P': 510,
'Nd': 7.3, 'F': 210, 'Sm': 2.63, 'Zr': 74, 'Hf': 2.05, 'Eu': 1.02, 'Sn': 1.1, 'Sb': 0.01, 'Ti': 7600,
'Gd': 3.68, 'Tb': 0.67, 'Dy': 4.55, 'Li': 4.3, 'Y': 28, 'Ho': 1.01, 'Er': 2.97, 'Tm': 0.456,
'Yb': 3.05, 'Lu': 0.455},
'UCC_Rudnick & Gao2003':{'K':23244.13676,'Ti':3835.794545,'P':654.6310022,'Li':24,'Be':2.1,'B':17,'N':83,'F':557,'S':62,'Cl':360,'Sc':14,'V':97,'Cr':92,
'Co':17.3,'Ni':47,'Cu':28,'Zn':67,'Ga':17.5,'Ge':1.4,'As':4.8,'Se':0.09,
'Br':1.6,'Rb':84,'Sr':320,'Y':21,'Zr':193,'Nb':12,'Mo':1.1,'Ru':0.34,
'Pd':0.52,'Ag':53,'Cd':0.09,'In':0.056,'Sn':2.1,'Sb':0.4,'I':1.4,'Cs':4.9,
'Ba':628,'La':31,'Ce':63,'Pr':7.1,'Nd':27,'Sm':4.7,'Eu':1,'Gd':4,'Tb':0.7,
'Dy':3.9,'Ho':0.83,'Er':2.3,'Tm':0.3,'Yb':1.96,'Lu':0.31,'Hf':5.3,'Ta':0.9,
'W':1.9,'Re':0.198,'Os':0.031,'Ir':0.022,'Pt':0.5,'Au':1.5,'Hg':0.05,'Tl':0.9,
'Pb':17,'Bi':0.16,'Th':10.5,'U':2.7}}
AllLabel = []
def __init__(self, parent=None, df=pd.DataFrame(),Standard={}):
QMainWindow.__init__(self, parent)
self.setWindowTitle('Trace Standardlized Pattern Diagram')
self.FileName_Hint='Trace'
#self._df = df
self._df_back =df
self.data_to_norm = self.CleanDataFile(df)
self._df = self.CleanDataFile(df)
self._given_Standard = self.Standard
if (len(df) > 0):
self._changed = True
# print('DataFrame recieved to Trace')
self.AllLabel=[]
for i in range(len(self._df)):
tmp_label = self._df.at[i, 'Label']
if tmp_label not in self.AllLabel:
self.AllLabel.append(tmp_label)
self.Element = [u'', u'Cs', u'Tl', u'Rb', u'Ba', u'W', u'Th', u'U', u'Nb', u'Ta', u'K', u'La', u'Ce', u'Pb', u'Pr',
u'Mo',
u'Sr', u'P', u'Nd', u'F', u'Sm', u'Zr', u'Hf', u'Eu', u'Sn', u'Sb', u'Ti', u'Gd', u'Tb', u'Dy',
u'Li',
u'Y', u'Ho', u'Er', u'Tm', u'Yb', u'Lu']
self.WholeData = []
self.X0 = 1
self.X1 = 36
self.X_Gap = 36
self.create_main_frame()
self.create_status_bar()
def Check(self):
row = self._df.index.tolist()
col = self._df.columns.tolist()
itemstocheck = self.itemstocheck
checklist = list((set(itemstocheck).union(set(col))) ^ (set(itemstocheck) ^ set(col)))
if len(checklist) > 1 :
self.OutPutCheck = True
else:
self.OutPutCheck = False
return(self.OutPutCheck)
def create_main_frame(self):
self.main_frame = QWidget()
self.dpi = 128
self.fig = Figure((18.0, 12.0), dpi=self.dpi)
self.fig.subplots_adjust(hspace=0.5, wspace=0.5, left=0.1, bottom=0.2, right=0.8, top=0.9)
self.canvas = FigureCanvas(self.fig)
self.canvas.setParent(self.main_frame)
self.axes = self.fig.add_subplot(111)
#self.axes.axis('off')
# Create the navigation toolbar, tied to the canvas
self.mpl_toolbar = NavigationToolbar(self.canvas, self.main_frame)
# Other GUI controls
self.save_img_button = QPushButton('&Save Img')
self.save_img_button.clicked.connect(self.saveImgFile)
self.explain_button = QPushButton('&Norm Result')
self.explain_button.clicked.connect(self.Explain)
self.Type_cb = QCheckBox('&Cs-Lu (36 Elements)')
self.Type_cb.setChecked(True)
self.Type_cb.stateChanged.connect(self.Trace) # int
self.type_slider_left_label = QLabel('Cs-Lu (36 Elements)')
self.type_slider_right_label= QLabel('Rb-Lu (26 Elements)')
self.type_slider = QSlider(Qt.Horizontal)
self.type_slider.setRange(0, 1)
self.type_slider.setValue(0)
self.type_slider.setTracking(True)
self.type_slider.setTickPosition(QSlider.TicksBothSides)
self.type_slider.valueChanged.connect(self.Trace) # int
self.legend_cb = QCheckBox('&Legend')
self.legend_cb.setChecked(True)
self.legend_cb.stateChanged.connect(self.Trace) # int
self.show_data_index_cb = QCheckBox('&Show Data Index')
self.show_data_index_cb.setChecked(False)
self.show_data_index_cb.stateChanged.connect(self.Trace) # int
self.standard_slider = QSlider(Qt.Horizontal)
self.standard_slider.setRange(0, len(self.StandardsName))
if len(self._given_Standard) > 0:
self.standard_slider.setValue(len(self.StandardsName))
self.right_label = QLabel("Self Defined Standard")
else:
self.standard_slider.setValue(0)
self.right_label = QLabel(self.StandardsName[int(self.standard_slider.value())])
self.standard_slider.setTracking(True)
self.standard_slider.setTickPosition(QSlider.TicksBothSides)
self.standard_slider.valueChanged.connect(self.Trace) # int
self.left_label= QLabel('Standard' )
self.item_left_label= QLabel('Show All' )
self.item_slider = QSlider(Qt.Horizontal)
self.item_slider.setRange(0, len(self.AllLabel))
self.item_slider.setTracking(True)
self.item_slider.setTickPosition(QSlider.TicksBothSides)
self.item_slider.valueChanged.connect(self.Trace) # int
# Layout with box sizers
#
self.hbox1 = QHBoxLayout()
self.hbox2 = QHBoxLayout()
for w in [self.save_img_button,self.explain_button,self.legend_cb,self.show_data_index_cb,
self.type_slider_left_label, self.type_slider,self.type_slider_right_label,
self.left_label, self.standard_slider,self.right_label]:
self.hbox1.addWidget(w)
self.hbox1.setAlignment(w, Qt.AlignVCenter)
for w in [self.item_left_label,self.item_slider]:
self.hbox2.addWidget(w)
self.hbox2.setAlignment(w, Qt.AlignVCenter)
self.vbox = QVBoxLayout()
self.vbox.addWidget(self.mpl_toolbar)
self.vbox.addWidget(self.canvas)
self.vbox.addLayout(self.hbox1)
self.vbox.addLayout(self.hbox2)
self.textbox = GrowingTextEdit(self)
self.vbox.addWidget(self.textbox)
self.main_frame.setLayout(self.vbox)
self.setCentralWidget(self.main_frame)
w=self.width()
h=self.height()
#setFixedWidth(int(w/10))
self.type_slider.setFixedWidth(int(w/10))
self.standard_slider.setMinimumWidth(int(w/4))
self.right_label.setMinimumWidth(int(w/10))
self.item_left_label.setFixedWidth(int(w/10))
def Trace(self, Left=0, Right=16, X0=1, X1=15, X_Gap=15, Base=-1,
Top=6, Y0=-1,
Y1=3, Y_Gap=5, FontSize=6,
xLabel=r'$Trace-Standardlized-Pattern$', yLabel='', width=12, height=12, dpi=300):
if (int(self.type_slider.value()) == 0):
self.Element = [u'', u'Cs', u'Tl', u'Rb', u'Ba', u'W', u'Th', u'U', u'Nb', u'Ta', u'K', u'La', u'Ce', u'Pb',
u'Pr', u'Mo',
u'Sr', u'P', u'Nd', u'F', u'Sm', u'Zr', u'Hf', u'Eu', u'Sn', u'Sb', u'Ti', u'Gd', u'Tb',
u'Dy', u'Li', u'Y', u'Ho', u'Er', u'Tm', u'Yb', u'Lu']
CommonElements = [i for i in self.Element if i in self._df.columns]
self.Element = CommonElements
self.xticks = [i for i in range(1,len(CommonElements)+2)]
self.xticklabels = CommonElements
self.setWindowTitle('Trace Standardlized Pattern Diagram Cs-Lu '+ str(len(CommonElements)+1) +' Elements')
else:
self.Type_cb.setText('&Rb-Lu (26 Elements)')
self.Element = [u'',u'Rb', u'Ba', u'Th', u'U', u'Nb', u'Ta', u'K', u'La', u'Ce', u'Pr', u'Sr', u'P', u'Nd',
u'Zr', u'Hf',
u'Sm', u'Eu', u'Ti', u'Tb', u'Dy', u'Y', u'Ho', u'Er', u'Tm', u'Yb', u'Lu']
CommonElements = [i for i in self.Element if i in self._df.columns]
self.Element = CommonElements
self.xticks = [i for i in range(1,len(CommonElements)+2)]
self.xticklabels = CommonElements
self.setWindowTitle('Trace Standardlized Pattern Diagram Rb-Lu '+ str(len(CommonElements)+1) +' Elements')
self.axes.clear()
#self.axes.axis('off')
self.axes.spines['right'].set_color('none')
self.axes.spines['top'].set_color('none')
self.WholeData = []
raw = self._df
#raw = self.CleanDataFile(self._df)
self.FontSize = FontSize
PointLabels = []
k = 0
flag = 1
slider_value=int(self.standard_slider.value())
item_value=int(self.item_slider.value())
if slider_value < len(self.StandardsName):
standardnamechosen = self.StandardsName[slider_value]
standardchosen = self.Standards[standardnamechosen]
self.textbox.setText(self.reference+"\nStandard Chosen: "+self.StandardsName[slider_value])
right_label_text=self.StandardsName[slider_value]
elif len(self._given_Standard)<=0:
standardnamechosen = self.StandardsName[slider_value-1]
standardchosen = self.Standards[standardnamechosen]
self.textbox.setText(self.reference+"\nStandard Chosen: "+self.StandardsName[slider_value-1])
right_label_text = self.StandardsName[slider_value-1]
else:
standardchosen = self._given_Standard
self.textbox.setText(self.reference + "\n You are using Self Defined Standard")
right_label_text = "Self Defined Standard"
self.right_label.setText(right_label_text)
Y_bottom = 0
Y_top = 0
for i in range(len(raw)):
for j in range(len(CommonElements)):
flag = 1
tmp = 1
if CommonElements[j] in raw.columns:
tmp = raw.at[i, CommonElements[j]] / standardchosen[CommonElements[j]]
elif CommonElements[j] == 'K' and 'K2O' in raw.columns:
tmp = raw.at[i, 'K2O'] * (
2 * 39.0983 / 94.1956) * 10000 / standardchosen[
CommonElements[j]]
elif CommonElements[j] == 'Ti' and 'TiO2' in raw.columns:
tmp = raw.at[i, 'TiO2'] * (
47.867 / 79.865) * 10000 / standardchosen[
CommonElements[j]]
else:
flag = 0
if flag == 1:
if tmp == tmp: # to delete nan
self.data_to_norm.at[i, self.Element[j]] = tmp
tmpflag = 1
a = 0
try:
a = math.log(tmp, 10)
except(ValueError):
tmpflag = 0
pass
if (tmpflag == 1):
if Y_bottom > a: Y_bottom = a
if Y_top < a: Y_top = a
self.axes.set_ylim(Y_bottom, Y_top)
if item_value == 0:
self.item_left_label.setText('Show All')
for i in range(len(raw)):
# raw.at[i, 'DataType'] == 'User' or raw.at[i, 'DataType'] == 'user' or raw.at[i, 'DataType'] == 'USER'
TmpLabel = ''
LinesX = []
LinesY = []
for j in range(len(CommonElements)):
flag = 1
tmp = 1
if CommonElements[j] in raw.columns:
tmp = raw.at[i, CommonElements[j]] / standardchosen[CommonElements[j]]
elif CommonElements[j] == 'K' and 'K2O' in raw.columns:
tmp = raw.at[i, 'K2O'] * (
2 * 39.0983 / 94.1956) * 10000 / standardchosen[
CommonElements[j]]
elif CommonElements[j] == 'Ti' and 'TiO2' in raw.columns:
tmp = raw.at[i, 'TiO2'] * (
47.867 / 79.865) * 10000 / standardchosen[
CommonElements[j]]
else:
flag = 0
if flag == 1:
if tmp==tmp:# to delete nan
self.data_to_norm.at[i, self.Element[j]] = tmp
tmpflag = 1
a=0
try:
a=math.log(tmp, 10)
except(ValueError):
tmpflag=0
pass
if(tmpflag==1):
LinesY.append(a)
LinesX.append(j + 1)
self.WholeData.append(math.log(tmp, 10))
if (raw.at[i, 'Label'] in PointLabels or raw.at[i, 'Label'] == ''):
TmpLabel = ''
else:
PointLabels.append(raw.at[i, 'Label'])
TmpLabel = raw.at[i, 'Label']
self.axes.scatter(j + 1, math.log(tmp, 10), marker=raw.at[i, 'Marker'],
s=raw.at[i, 'Size'], color=raw.at[i, 'Color'], alpha=raw.at[i, 'Alpha'],
label=TmpLabel)
self.axes.plot(LinesX, LinesY, color=raw.at[i, 'Color'], linewidth=raw.at[i, 'Width'],
linestyle=raw.at[i, 'Style'], alpha=raw.at[i, 'Alpha'])
if (self.show_data_index_cb.isChecked()):
if 'Index' in self._df_back.columns.values:
self.axes.annotate(self._df_back.at[i, 'Index'],
xy=(LinesX[-1],
LinesY[-1]),
color=self._df.at[i, 'Color'],
alpha=self._df.at[i, 'Alpha'])
else:
self.axes.annotate('No' + str(i + 1),
xy=(LinesX[-1],
LinesY[-1]),
color=self._df.at[i, 'Color'],
alpha=self._df.at[i, 'Alpha'])
else:
self.item_left_label.setText(self.AllLabel[item_value-1])
for i in range(len(raw)):
# raw.at[i, 'DataType'] == 'User' or raw.at[i, 'DataType'] == 'user' or raw.at[i, 'DataType'] == 'USER'
TmpLabel = ''
LinesX = []
LinesY = []
if raw.at[i, 'Label'] == self.AllLabel[item_value - 1]:
alpha = raw.at[i, 'Alpha']
linewidth = raw.at[i, 'Width']
pointsize = raw.at[i, 'Size']
for j in range(len(CommonElements)):
flag = 1
tmp = 1
if CommonElements[j] in raw.columns:
tmp = raw.at[i, CommonElements[j]] / standardchosen[CommonElements[j]]
elif CommonElements[j] == 'K' and 'K2O' in raw.columns:
tmp = raw.at[i, 'K2O'] * (
2 * 39.0983 / 94.1956) * 10000 / standardchosen[
CommonElements[j]]
elif CommonElements[j] == 'Ti' and 'TiO2' in raw.columns:
tmp = raw.at[i, 'TiO2'] * (
47.867 / 79.865) * 10000 / standardchosen[
CommonElements[j]]
else:
flag = 0
if flag == 1:
if tmp==tmp:# to delete nan
self.data_to_norm.at[i, self.Element[j]] = tmp
tmpflag = 1
a=0
try:
a=math.log(tmp, 10)
except(ValueError):
tmpflag=0
pass
if(tmpflag==1):
LinesY.append(a)
LinesX.append(j + 1)
self.WholeData.append(math.log(tmp, 10))
if (raw.at[i, 'Label'] in PointLabels or raw.at[i, 'Label'] == ''):
TmpLabel = ''
else:
PointLabels.append(raw.at[i, 'Label'])
TmpLabel = raw.at[i, 'Label']
self.axes.scatter(j + 1, math.log(tmp, 10), marker=raw.at[i, 'Marker'],
s=raw.at[i, 'Size'], color=raw.at[i, 'Color'], alpha=raw.at[i, 'Alpha'],
label=TmpLabel)
self.axes.plot(LinesX, LinesY, color=raw.at[i, 'Color'], linewidth=raw.at[i, 'Width'],
linestyle=raw.at[i, 'Style'], alpha=raw.at[i, 'Alpha'])
if (self.show_data_index_cb.isChecked()):
if 'Index' in self._df_back.columns.values:
self.axes.annotate(self._df_back.at[i, 'Index'],
xy=(LinesX[-1],
LinesY[-1]),
color=self._df.at[i, 'Color'],
alpha=self._df.at[i, 'Alpha'])
else:
self.axes.annotate('No' + str(i + 1),
xy=(LinesX[-1],
LinesY[-1]),
color=self._df.at[i, 'Color'],
alpha=self._df.at[i, 'Alpha'])
Tale = 0
Head = 0
if (len(self.WholeData) > 0):
Tale = min(self.WholeData)
Head = max(self.WholeData)+0.5
Location = round(Tale - (Head - Tale) / 5)
count = round((Head - Tale) / 5 * 7) + 1
if (self.legend_cb.isChecked()):
self.axes.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0, prop=fontprop)
self.yticks = [Location+i for i in range(count)]
self.yticklabels = [str(np.power(10.0, (Location + i))) for i in range(count)]
self.axes.set_yticks(self.yticks)
self.axes.set_yticklabels(self.yticklabels, fontsize=6)
self.axes.set_xticks(self.xticks)
self.xticklabels.append( '') # fix blank head problem by matplotlib
self.axes.set_xticklabels(self.xticklabels, rotation=-45, fontsize=6)
self.canvas.draw()
self.OutPutTitle='Trace'
self.OutPutFig=self.fig
def Explain(self):
self.data_to_norm
for i in self.data_to_norm.columns.values.tolist():
if i in self.Element:
self.data_to_norm = self.data_to_norm.rename(columns={i: i + '_N'})
elif i in ['Label', 'Number', 'Tag', 'Name', 'Author', 'DataType', 'Marker', 'Color', 'Size', 'Alpha',
'Style', 'Width']:
pass
else:
self.data_to_norm = self.data_to_norm.drop(i,axis=1)
self.OutPutData = self.data_to_norm.set_index('Label')
self.tablepop = TableViewer(df=self.OutPutData,title='Trace Element Norm Result')
self.tablepop.show()