def FillSurveys(self):
self.AS=AllSurveys(self.ODB)
FullName=self.AS.GetCombo()
for fn in FullName:
item=QListWidgetItem(fn)
self.AvailSurveys.addItem(item)
self.AvailSurveys.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
class Ui_Dialog(object):
def __init__(self,Dialog,ODB,OUTmdb):
self.setupUi(Dialog)
self.inMDB=ODB
self.resultODB=OUTmdb
self.OUTmdb=self.resultODB.ODB
self.ODB=self.inMDB.ODB
self.FillSurveys()
self.FillTranChar()
self.MakeConnect()
self.DefaultSettings()
def setupUi(self, Dialog):
Dialog.setObjectName(_fromUtf8("Dialog"))
Dialog.resize(692, 769)
font = QtGui.QFont()
font.setPointSize(12)
Dialog.setFont(font)
self.AllSurveys = QtGui.QCheckBox(Dialog)
self.AllSurveys.setGeometry(QtCore.QRect(30, 224, 141, 41))
self.AllSurveys.setStyleSheet(_fromUtf8("font: 12pt \"MS Shell Dlg 2\";"))
self.AllSurveys.setObjectName(_fromUtf8("AllSurveys"))
self.label = QtGui.QLabel(Dialog)
self.label.setGeometry(QtCore.QRect(30, 4, 241, 31))
self.label.setObjectName(_fromUtf8("label"))
self.label_2 = QtGui.QLabel(Dialog)
self.label_2.setGeometry(QtCore.QRect(290, 4, 241, 31))
self.label_2.setObjectName(_fromUtf8("label_2"))
self.groupBox_2 = QtGui.QGroupBox(Dialog)
self.groupBox_2.setGeometry(QtCore.QRect(20, 284, 131, 241))
font = QtGui.QFont()
font.setPointSize(8)
self.groupBox_2.setFont(font)
self.groupBox_2.setObjectName(_fromUtf8("groupBox_2"))
self.USB50 = QtGui.QRadioButton(self.groupBox_2)
self.USB50.setGeometry(QtCore.QRect(30, 210, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB50.setFont(font)
self.USB50.setAutoExclusive(False)
self.USB50.setObjectName(_fromUtf8("USB50"))
self.NumberBootstrapLabel = QtGui.QLabel(Dialog)
self.NumberBootstrapLabel.setGeometry(QtCore.QRect(430, 290, 131, 41))
self.NumberBootstrapLabel.setWordWrap(True)
self.NumberBootstrapLabel.setObjectName(_fromUtf8("NumberBootstrapLabel"))
self.NumberBootstrap = QtGui.QPlainTextEdit(Dialog)
self.NumberBootstrap.setGeometry(QtCore.QRect(320, 290, 101, 31))
self.NumberBootstrap.setObjectName(_fromUtf8("NumberBootstrap"))
self.RandomSeed = QtGui.QPlainTextEdit(Dialog)
self.RandomSeed.setGeometry(QtCore.QRect(320, 340, 101, 31))
self.RandomSeed.setObjectName(_fromUtf8("RandomSeed"))
self.RandomSeedLabel = QtGui.QLabel(Dialog)
self.RandomSeedLabel.setGeometry(QtCore.QRect(430, 340, 131, 31))
self.RandomSeedLabel.setObjectName(_fromUtf8("RandomSeedLabel"))
self.USB89 = QtGui.QRadioButton(Dialog)
self.USB89.setGeometry(QtCore.QRect(51, 431, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB89.setFont(font)
self.USB89.setAutoExclusive(False)
self.USB89.setObjectName(_fromUtf8("USB89"))
self.USB69 = QtGui.QRadioButton(Dialog)
self.USB69.setGeometry(QtCore.QRect(51, 460, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB69.setFont(font)
self.USB69.setAutoExclusive(False)
self.USB69.setObjectName(_fromUtf8("USB69"))
self.USB99 = QtGui.QRadioButton(Dialog)
self.USB99.setGeometry(QtCore.QRect(51, 402, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB99.setFont(font)
self.USB99.setAutoExclusive(False)
self.USB99.setObjectName(_fromUtf8("USB99"))
self.USB1000 = QtGui.QRadioButton(Dialog)
self.USB1000.setGeometry(QtCore.QRect(51, 315, 59, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB1000.setFont(font)
self.USB1000.setAutoExclusive(False)
self.USB1000.setObjectName(_fromUtf8("USB1000"))
self.USB140 = QtGui.QRadioButton(Dialog)
self.USB140.setGeometry(QtCore.QRect(51, 344, 51, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB140.setFont(font)
self.USB140.setAutoExclusive(False)
self.USB140.setObjectName(_fromUtf8("USB140"))
self.USB119 = QtGui.QRadioButton(Dialog)
self.USB119.setGeometry(QtCore.QRect(51, 373, 51, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB119.setFont(font)
self.USB119.setAutoExclusive(False)
self.USB119.setObjectName(_fromUtf8("USB119"))
self.AvailSurveys = QtGui.QListWidget(Dialog)
self.AvailSurveys.setGeometry(QtCore.QRect(21, 35, 256, 192))
self.AvailSurveys.setObjectName(_fromUtf8("AvailSurveys"))
self.TransectCharacteristics = QtGui.QListWidget(Dialog)
self.TransectCharacteristics.setGeometry(QtCore.QRect(320, 35, 256, 111))
self.TransectCharacteristics.setObjectName(_fromUtf8("TransectCharacteristics"))
self.DoCalcs = QtGui.QPushButton(Dialog)
self.DoCalcs.setGeometry(QtCore.QRect(190, 440, 91, 41))
self.DoCalcs.setObjectName(_fromUtf8("DoCalcs"))
self.QuitBttn = QtGui.QPushButton(Dialog)
self.QuitBttn.setGeometry(QtCore.QRect(320, 440, 91, 41))
self.QuitBttn.setObjectName(_fromUtf8("QuitBttn"))
self.MinDepthLabel = QtGui.QLabel(Dialog)
self.MinDepthLabel.setGeometry(QtCore.QRect(430, 180, 131, 31))
self.MinDepthLabel.setWordWrap(True)
self.MinDepthLabel.setObjectName(_fromUtf8("MinDepthLabel"))
self.MinDepth = QtGui.QPlainTextEdit(Dialog)
self.MinDepth.setGeometry(QtCore.QRect(320, 180, 101, 31))
self.MinDepth.setObjectName(_fromUtf8("MinDepth"))
self.MaxDepth = QtGui.QPlainTextEdit(Dialog)
self.MaxDepth.setGeometry(QtCore.QRect(320, 230, 101, 31))
self.MaxDepth.setObjectName(_fromUtf8("MaxDepth"))
self.MaxDepthLabel = QtGui.QLabel(Dialog)
self.MaxDepthLabel.setGeometry(QtCore.QRect(430, 230, 131, 31))
self.MaxDepthLabel.setWordWrap(True)
self.MaxDepthLabel.setObjectName(_fromUtf8("MaxDepthLabel"))
self.retranslateUi(Dialog)
QtCore.QMetaObject.connectSlotsByName(Dialog)
def retranslateUi(self, Dialog):
Dialog.setWindowTitle(_translate("Dialog", "Red Sea Urchin Analysis Program", None))
self.AllSurveys.setText(_translate("Dialog", "Do All Surveys?", None))
self.label.setText(_translate("Dialog", "<html><head/><body><p align=\"center\"><span style=\" font-size:9pt;\">Data to Analyze [Source] [Year] [Location]:</span></p></body></html>", None))
self.label_2.setText(_translate("Dialog", "<html><head/><body><p align=\"center\"><span style=\" font-size:9pt;\">Analyze by:</span></p></body></html>", None))
self.groupBox_2.setTitle(_translate("Dialog", "Upper Size Bounds (mm)", None))
self.USB50.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB50.setText(_translate("Dialog", "50", None))
self.NumberBootstrapLabel.setText(_translate("Dialog", "<html><head/><body><p><span style=\" font-size:10pt;\">Number of Bootstrap Repititions</span></p></body></html>", None))
self.RandomSeedLabel.setText(_translate("Dialog", "<html><head/><body><p><span style=\" font-size:10pt;\">Random Seed</span></p></body></html>", None))
self.USB89.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB89.setText(_translate("Dialog", "89", None))
self.USB69.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB69.setText(_translate("Dialog", "69", None))
self.USB99.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB99.setText(_translate("Dialog", "99", None))
self.USB1000.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB1000.setText(_translate("Dialog", "1000", None))
self.USB140.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB140.setText(_translate("Dialog", "140", None))
self.USB119.setToolTip(_translate("Dialog", "<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>", None))
self.USB119.setText(_translate("Dialog", "119", None))
self.DoCalcs.setText(_translate("Dialog", "Do\n"
"Calculations", None))
self.QuitBttn.setText(_translate("Dialog", "Quit", None))
self.MinDepthLabel.setText(_translate("Dialog", "<html><head/><body><p><span style=\" font-size:10pt;\">Minimum Depth (m)</span></p></body></html>", None))
self.MaxDepthLabel.setText(_translate("Dialog", "<html><head/><body><p><span style=\" font-size:10pt;\">Maximum Depth (m)</span></p></body></html>", None))
def FillSurveys(self):
self.AS=AllSurveys(self.ODB)
FullName=self.AS.GetCombo()
for fn in FullName:
item=QListWidgetItem(fn)
self.AvailSurveys.addItem(item)
self.AvailSurveys.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
def FillTranChar(self):
for fieldname in ['SurveyTitle','Location','SiteNum','Year','StatArea','SubArea','InBed']:
item=QListWidgetItem(fieldname)
self.TransectCharacteristics.addItem(item)
self.TransectCharacteristics.setSelectionMode(QtGui.QAbstractItemView.MultiSelection)
def MakeConnect(self):
self.DoCalcs.clicked.connect(self.Calculations)
self.QuitBttn.clicked.connect(self.QuitCalcs)
self.AllSurveys.stateChanged.connect(self.DoAllSurveys)
self.TransectCharacteristics.itemSelectionChanged.connect(self.CoordStatAreaSubArea)
def Calculations(self):
print ('Calculations Started')
seed(int(self.RandomSeed.document().toPlainText()))
self.GetSelectedSurveys()
self.GetSelectedTranChar()
self.GetSelectedUppSizeBound()
self.TranClassChar=MetaTransectClass(self.ODB,\
self.SelectedSurveys,\
self.SelectedTranchar )
self.PrepOUTmdb()
dictSelectedSurveys=self.SelectedSurveystoDict()
CopyMDB(self.ODB, self.OUTmdb ,dictSelectedSurveys)
CB=[99,95,90,75,50]
nboot=int(self.NumberBootstrap.document().toPlainText())
for i in range(self.TranClassChar.nclass):
FTC=self.TranClassChar.FormatTranClass(i)
print('\n')
if FTC['SurveyTitle']!='Combined': print('SurveyTitle: ',FTC['SurveyTitle' ])
if FTC['Location' ]!='Combined': print('Location: ',FTC['Location' ])
if FTC['Year' ]!=MinInt: print('Year: ',FTC['Year' ])
if FTC['Site' ]!=MinInt: print('Site: ',FTC['Site' ])
if FTC['StatArea' ]!=MinInt: print('StatArea: ',FTC['StatArea'] )
if FTC['SubArea' ]!=MinInt: print('SubArea: ',FTC['SubArea' ] )
print(len(self.TranClassChar.key[i]), ' transects')
tc=transectclass(self.ODB,self.TranClassChar.key[i],self.TranClassChar.Allo[i],QueryFunc,\
SizeBound=self.UppSizeBnd,\
MinDepth=float(self.MinDepth.document().toPlainText()),\
MaxDepth=float(self.MaxDepth.document().toPlainText()))
CurDeterm=tc.GetFormatEstVal()
CurCB=tc.GetPctCB(CB,nboot=nboot)
#Transect Classes
self.OUTmdb.ADDTo_TranChar(FTC['SurveyTitle'],FTC['Location'],FTC['SiteNum'],FTC['Year'],FTC['StatArea'],FTC['SubArea'],FTC['InBed'],FTC['NumTran'],\
tc.GetSurveyedArea(),tc.GetNumSurveyedQuadInDepthRange())
tck=self.OUTmdb.GetTranCharKey(FTC['SurveyTitle'],FTC['Location'],FTC['SiteNum'],FTC['Year'],FTC['StatArea'],FTC['SubArea'],FTC['InBed'])
tc.WriteTransectResults(self.OUTmdb,tck)
#The confidence bounds
if (CurCB!=None):
for cbResult in CurCB:
CBval=cbResult['CB']
SN=list(filter(lambda x:x!='CB', cbResult.keys()))
for sn in SN:
CurSize=cbResult[sn]
SK=self.OUTmdb.GetSizeRangeKey(CurSize['SizeLimit'][-1])
self.OUTmdb.ADDTo_ConfInterval(\
tck,SK,\
CBval,\
CurSize['linear']['Pop'][0], CurSize['linear']['Pop'][1], \
CurSize['spatial']['Pop'][0], CurSize['spatial']['Pop'][1], \
CurSize['linear']['Bmass'][0], CurSize['linear']['Bmass'][1], \
CurSize['spatial']['Bmass'][0], CurSize['spatial']['Bmass'][1])
#The estimated values
for sn in CurDeterm.keys():
CurSize=CurDeterm[sn]
SK=self.OUTmdb.GetSizeRangeKey(CurSize['SizeLimit'][-1])
self.OUTmdb.ADDTo_EstDens(\
CurSize['linear']['Pop'],CurSize['spatial']['Pop'],\
CurSize['linear']['Bmass'],CurSize['spatial']['Bmass'],\
TranCharKey=tck,SizeKey=SK)
print('\ndone MainWindow Line 274')
def GetSelectedUppSizeBound(self):
self.UppSizeBnd=[]
if self.USB50.isChecked() :self.UppSizeBnd+=[50 ]
if self.USB69.isChecked() :self.UppSizeBnd+=[69 ]
if self.USB89.isChecked() :self.UppSizeBnd+=[89 ]
if self.USB99.isChecked() :self.UppSizeBnd+=[99 ]
if self.USB119.isChecked():self.UppSizeBnd+=[119]
if self.USB140.isChecked():self.UppSizeBnd+=[140]
self.UppSizeBnd+=[inf]
def GetSelectedTranChar(self):
self.SelectedTranchar=[]
for index in range(self.TransectCharacteristics.count()):
if self.TransectCharacteristics.item(index).isSelected():
self.SelectedTranchar+=[self.TransectCharacteristics.item(index).text()]
def GetSelectedSurveys(self):
self.SelectedSurveys=[]
year=self.AS.GetYear()
survey=self.AS.GetSurvey()
for index in range(self.AvailSurveys.count()):
if self.AvailSurveys.item(index).isSelected():
self.SelectedSurveys+=[[survey[index],year[index]]]
def DoAllSurveys(self):
if self.AllSurveys.isChecked():
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(True)
else:
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(False)
def CoordStatAreaSubArea(self):
'''Make sure statarea and subarea are coherent'''
#Update list of selected transect-characteristics
self.GetSelectedTranChar()
#if subarea is selected, force statarea to be selected
if ('SubArea' in self.SelectedTranchar) and not('StatArea' in self.SelectedTranchar) :
for index in range(self.TransectCharacteristics.count()):
if self.TransectCharacteristics.item(index).text()=='StatArea':
self.TransectCharacteristics.item(index).setSelected(True)
self.GetSelectedTranChar()
def QuitCalcs(self):
print ('No Calculations')
sys.exit(app.exec_())
def DefaultSettings(self):
self.NumberBootstrap.insertPlainText('10000')
self.RandomSeed.insertPlainText('756')
self.MinDepth.insertPlainText('-1000')
self.MaxDepth.insertPlainText('1000')
self.USB1000.setDisabled(True)
self.USB1000.setChecked(True)
self.USB89.setChecked(True)
def PrepOUTmdb(self):
'''Put information into output. Not the stats - just the metadata'''
self.OUTmdb.ADDTo_Analysis(int(self.NumberBootstrap.document().toPlainText()),\
int(self.RandomSeed.document().toPlainText()),\
float(self.MinDepth.document().toPlainText()),\
float(self.MaxDepth.document().toPlainText()))
self.OUTmdb.ADDTo_SizeRange(0,self.UppSizeBnd[0])
for x in range(1,len(self.UppSizeBnd)):
self.OUTmdb.SizeRangeKey.Increment()
self.OUTmdb.ADDTo_SizeRange(1+self.UppSizeBnd[x-1],self.UppSizeBnd[x] )
for sy in self.SelectedSurveys:
self.OUTmdb.ADDTo_SurveyUsed(sy[0],sy[1])
def SelectedSurveystoDict(self):
'''Convert self.SelectedSurveys as a list of dictionaries'''
if isinstance(self.SelectedSurveys[0],dict):
return(self.SelectedSurveys)
result=[{'Location':t[0], 'Year':t[1]} for t in self.SelectedSurveys]
return(result)
class SCmain(QMainWindow, Ui_MainWindow):
def __init__(self, ODB, OUTmdb, parent=None):
self.inMDB = ODB
self.resultODB = OUTmdb
QMainWindow.__init__(self, parent)
self.setupUi(self)
self.MakeConnect()
self.OUTmdb = self.resultODB.ODB
self.ODB = self.inMDB.ODB
self.FillSurveys()
self.FillTranChar()
self.MakeConnect()
self.DefaultSettings()
def FillSurveys(self):
self.AS = AllSurveys(self.ODB)
FullName = self.AS.GetCombo()
for fn in FullName:
item = QListWidgetItem(fn)
self.AvailSurveys.addItem(item)
self.AvailSurveys.setSelectionMode(
QtGui.QAbstractItemView.MultiSelection)
def FillTranChar(self):
for fieldname in ['Project', 'Site', 'Year', 'StatArea', 'SubArea']:
item = QListWidgetItem(fieldname)
self.TransectCharacteristics.addItem(item)
self.TransectCharacteristics.setSelectionMode(
QtGui.QAbstractItemView.MultiSelection)
def MakeConnect(self):
self.DoCalcs.clicked.connect(self.Calculations)
self.QuitBttn.clicked.connect(self.QuitCalcs)
self.AllSurveys.stateChanged.connect(self.DoAllSurveys)
def Calculations(self):
#Do nothing unless some surveys are selected
if self.AvailSurveys.count() == 0: return
seed(int(self.RandomSeed.document().toPlainText()))
try:
self.GetSelectedSurveys()
except:
self.QuitCalcs()
#copy stubs of input tables to the output file.
dictSelectedSurveys = self.SelectedSurveystoDict()
CopyMDB(self.ODB, self.OUTmdb, dictSelectedSurveys)
print('\nCalculations Started')
self.GetSelectedTranChar()
self.TranClassChar=MetaTransectClass(self.ODB,\
self.SelectedSurveys,\
self.SelectedTranchar)
CB = [99, 95, 90, 75, 50]
self.Comments = self.RunComments.document().toPlainText()
self.nboot = int(self.NumberBootstrap.document().toPlainText())
self.seed = int(self.RandomSeed.document().toPlainText())
self.LeastDepth = float(self.MinDepth.document().toPlainText())
self.MostDepth = float(self.MaxDepth.document().toPlainText())
self.SourceMeanWeight = 'LogBook'
if self.MarketSample.isChecked():
self.SourceMeanWeight = 'MarketSample'
if self.Biodata.isChecked(): self.SourceMeanWeight = 'Biodata'
self.species = 'californicus'
import californicusQueryFunc as QueryFunc
if self.miniata.isChecked():
self.species = 'miniata'
import miniataQueryFunc as QueryFunc
if self.pallida.isChecked():
self.species = 'pallida'
import pallidaQueryFunc as QueryFunc
AlloSource = QueryFunc.AlloEqn()
self.PrepOUTmdb()
SiteCB = []
SiteEst = []
for i in range(self.TranClassChar.nclass):
FMT = self.TranClassChar.FormatTranClass(i)
print('\n')
if FMT['Project'] != 'Combined':
print('Project: ', FMT['Project'])
if FMT['Site'] != MinInt: print('Site: ', FMT['Site'])
if FMT['Year'] != MinInt: print('Year: ', FMT['Year'])
if FMT['StatArea'] != MinInt: print('StatArea: ', FMT['StatArea'])
if FMT['SubArea'] != MinInt: print('SubArea: ', FMT['SubArea'])
print('Reading Data')
CTC = CukeTransectclass(self.ODB,
i,
self.TranClassChar,
AlloSource,
QueryFunc,
MinDepth=self.LeastDepth,
MaxDepth=self.MostDepth)
print('NumTran: ', len(CTC.IndexTranUse))
self.OUTmdb.ADDTo_TranChar(FMT['Project'],FMT['Site'],FMT['Year'],FMT['StatArea'],FMT['SubArea'],FMT['NumTran'],\
CTC.GetSurveyedArea())
print('Writing results for individual transects')
CTC.WriteTransectResults(self.OUTmdb, FMT)
print('Writing estimated values')
SiteEst += [
CTC.WriteSiteResults(self.OUTmdb, FMT, self.SourceMeanWeight)
]
print('Calculating confidence bounds')
SiteCB += [
CTC.WriteSiteCB(self.OUTmdb, FMT, nboot=self.nboot, CB=CB)
]
self.OUTmdb.TranCharKey.Increment()
print('\nCombined')
if self.TranClassChar.nclass > 1:
self.WriteOverall(SiteEst, SiteCB, CB)
else:
FMT = self.TranClassChar.FormatTranClass(0)
dummy = CompositeAsTransectclass(CTC, SiteCB[0]['SampPopDensity'])
dummy.WriteCB(self.OUTmdb, FMT, CB=CB)
dummy.WriteResults(self.OUTmdb, FMT, self.SourceMeanWeight)
print('\ndone MainWindow Line 147')
return
def WriteOverall(self, SiteEst, SiteCB, CB, nlevel=100):
nsite = len(SiteCB)
#Estimated Values
EstPop = sum(list(map(lambda x: x['EstPop'], SiteEst)))
EstBma = sum(list(map(lambda x: x['EstBma'], SiteEst)))
CL = sum(list(map(lambda x: x['CL'], SiteEst)))
PopDens = EstPop / CL
BmaDens = EstBma / CL
self.OUTmdb.ADDTo_Results_Overall(PopDens, EstPop, BmaDens, EstBma)
#Confidence Bounds
CBoverall = CalcOverallStats(SiteCB,
newq=None,
randomize=True,
CB=CB,
nlevel=nlevel)
if nsite == 1:
CBoverall['PopDensCB'] = Naive_CB(SiteEst[0]['PopDens'], CB=CB)
CBoverall['BmaDens'] = Naive_CB(SiteEst[0]['BmaDens'], CB=CB)
for i in range(len(CB)):
self.OUTmdb.ADDTo_Results_OverallConfBounds(CB[i],\
CBoverall['PopDensCB'][i][0], CBoverall['PopDensCB'][i][1],\
CBoverall['TotaPopCB'][i][0], CBoverall['TotaPopCB'][i][1],\
CBoverall['BmaDensCB'][i][0], CBoverall['BmaDensCB'][i][1],\
CBoverall['TotaBmaCB'][i][0], CBoverall['TotaBmaCB'][i][1])
def GetSelectedTranChar(self):
self.SelectedTranchar = []
for index in range(self.TransectCharacteristics.count()):
if self.TransectCharacteristics.item(index).isSelected():
self.SelectedTranchar += [
self.TransectCharacteristics.item(index).text()
]
def GetSelectedSurveys(self):
self.SelectedSurveys = []
year = self.AS.GetYear()
survey = self.AS.GetSurvey()
for index in range(self.AvailSurveys.count()):
if self.AvailSurveys.item(index).isSelected():
self.SelectedSurveys += [[survey[index], year[index]]]
def DoAllSurveys(self):
if self.AllSurveys.isChecked():
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(True)
else:
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(False)
def QuitCalcs(self):
print('\nBye Bye')
os._exit(0)
quit()
sys.exit(app.exec_())
def DefaultSettings(self):
self.NumberBootstrap.insertPlainText('10000')
self.RandomSeed.insertPlainText('756')
self.MinDepth.insertPlainText('-1000')
self.MaxDepth.insertPlainText('1000')
self.californicus.setChecked(True)
self.MarketSample.setChecked(True)
def PrepOUTmdb(self):
'''Put information into output. Not the stats - just the metadata'''
self.OUTmdb.ADDTo_Results_Header(self.Comments, self.species,
str(self.nboot), str(self.seed),
str(self.LeastDepth),
str(self.MostDepth))
for ss in self.SelectedSurveys:
self.OUTmdb.ADDTo_SurveyUsed(ss[0], str(ss[1]))
def SelectedSurveystoDict(self):
'''Convert self.SelectedSurveys as a list of dictionaries'''
if isinstance(self.SelectedSurveys[0], dict):
return (self.SelectedSurveys)
result = [{
'Project': t[0],
'Year': t[1]
} for t in self.SelectedSurveys]
return (result)
class Ui_Dialog(object):
def __init__(self, Dialog, ODB, OUTmdb):
self.setupUi(Dialog)
self.inMDB = ODB
self.resultODB = OUTmdb
self.OUTmdb = self.resultODB.ODB
self.ODB = self.inMDB.ODB
#pdb.set_trace()
self.FillSurveys()
self.FillTranChar()
self.MakeConnect()
self.DefaultSettings()
def setupUi(self, Dialog):
Dialog.setObjectName(_fromUtf8("Dialog"))
Dialog.resize(692, 769)
font = QtGui.QFont()
font.setPointSize(12)
#pdb.set_trace()
Dialog.setFont(font)
self.AllSurveys = QtGui.QCheckBox(Dialog)
self.AllSurveys.setGeometry(QtCore.QRect(30, 224, 141, 41))
self.AllSurveys.setStyleSheet(
_fromUtf8("font: 12pt \"MS Shell Dlg 2\";"))
self.AllSurveys.setObjectName(_fromUtf8("AllSurveys"))
self.label = QtGui.QLabel(Dialog)
self.label.setGeometry(QtCore.QRect(30, 4, 241, 31))
self.label.setObjectName(_fromUtf8("label"))
self.label_2 = QtGui.QLabel(Dialog)
self.label_2.setGeometry(QtCore.QRect(290, 4, 241, 31))
self.label_2.setObjectName(_fromUtf8("label_2"))
self.CalculateAllometric = QtGui.QCheckBox(Dialog)
self.CalculateAllometric.setGeometry(QtCore.QRect(320, 160, 241, 61))
self.CalculateAllometric.setStyleSheet(
_fromUtf8("font: 12pt \"MS Shell Dlg 2\";"))
self.CalculateAllometric.setObjectName(
_fromUtf8("CalculateAllometric"))
self.label_4 = QtGui.QLabel(Dialog)
self.label_4.setGeometry(QtCore.QRect(320, 440, 321, 61))
self.label_4.setWordWrap(True)
self.label_4.setObjectName(_fromUtf8("label_4"))
self.intcpt = QtGui.QPlainTextEdit(Dialog)
self.intcpt.setGeometry(QtCore.QRect(320, 230, 191, 31))
self.intcpt.setObjectName(_fromUtf8("intcpt"))
self.intcptLabel = QtGui.QLabel(Dialog)
self.intcptLabel.setGeometry(QtCore.QRect(520, 230, 131, 31))
self.intcptLabel.setObjectName(_fromUtf8("intcptLabel"))
self.sdintcptLabel = QtGui.QLabel(Dialog)
self.sdintcptLabel.setGeometry(QtCore.QRect(520, 270, 131, 31))
self.sdintcptLabel.setObjectName(_fromUtf8("sdintcptLabel"))
self.sdintcpt = QtGui.QPlainTextEdit(Dialog)
self.sdintcpt.setGeometry(QtCore.QRect(320, 270, 191, 31))
self.sdintcpt.setObjectName(_fromUtf8("sdintcpt"))
self.sigmabetaLabel = QtGui.QLabel(Dialog)
self.sigmabetaLabel.setGeometry(QtCore.QRect(520, 350, 131, 31))
self.sigmabetaLabel.setObjectName(_fromUtf8("sigmabetaLabel"))
self.mubetaLabel = QtGui.QLabel(Dialog)
self.mubetaLabel.setGeometry(QtCore.QRect(520, 310, 131, 31))
self.mubetaLabel.setObjectName(_fromUtf8("mubetaLabel"))
self.sigmabeta = QtGui.QPlainTextEdit(Dialog)
self.sigmabeta.setGeometry(QtCore.QRect(320, 350, 191, 31))
self.sigmabeta.setObjectName(_fromUtf8("sigmabeta"))
self.mubeta = QtGui.QPlainTextEdit(Dialog)
self.mubeta.setGeometry(QtCore.QRect(320, 310, 191, 31))
self.mubeta.setObjectName(_fromUtf8("mubeta"))
self.sigmaepsilon = QtGui.QPlainTextEdit(Dialog)
self.sigmaepsilon.setGeometry(QtCore.QRect(320, 390, 191, 31))
self.sigmaepsilon.setObjectName(_fromUtf8("sigmaepsilon"))
self.sigmaepsilonLabel = QtGui.QLabel(Dialog)
self.sigmaepsilonLabel.setGeometry(QtCore.QRect(520, 390, 131, 31))
self.sigmaepsilonLabel.setObjectName(_fromUtf8("sigmaepsilonLabel"))
self.groupBox_2 = QtGui.QGroupBox(Dialog)
self.groupBox_2.setGeometry(QtCore.QRect(20, 284, 131, 201))
font = QtGui.QFont()
font.setPointSize(8)
self.groupBox_2.setFont(font)
self.groupBox_2.setObjectName(_fromUtf8("groupBox_2"))
self.NumberBootstrapLabel = QtGui.QLabel(Dialog)
self.NumberBootstrapLabel.setGeometry(QtCore.QRect(130, 560, 131, 41))
self.NumberBootstrapLabel.setWordWrap(True)
self.NumberBootstrapLabel.setObjectName(
_fromUtf8("NumberBootstrapLabel"))
self.NumberBootstrap = QtGui.QPlainTextEdit(Dialog)
self.NumberBootstrap.setGeometry(QtCore.QRect(20, 560, 101, 31))
self.NumberBootstrap.setObjectName(_fromUtf8("NumberBootstrap"))
self.RandomSeed = QtGui.QPlainTextEdit(Dialog)
self.RandomSeed.setGeometry(QtCore.QRect(310, 560, 101, 31))
self.RandomSeed.setObjectName(_fromUtf8("RandomSeed"))
self.RandomSeedLabel = QtGui.QLabel(Dialog)
self.RandomSeedLabel.setGeometry(QtCore.QRect(420, 560, 131, 31))
self.RandomSeedLabel.setObjectName(_fromUtf8("RandomSeedLabel"))
self.USB39 = QtGui.QRadioButton(Dialog)
self.USB39.setGeometry(QtCore.QRect(51, 431, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB39.setFont(font)
self.USB39.setAutoExclusive(False)
self.USB39.setObjectName(_fromUtf8("USB39"))
self.USB24 = QtGui.QRadioButton(Dialog)
self.USB24.setGeometry(QtCore.QRect(51, 460, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB24.setFont(font)
self.USB24.setAutoExclusive(False)
self.USB24.setObjectName(_fromUtf8("USB24"))
self.USB54 = QtGui.QRadioButton(Dialog)
self.USB54.setGeometry(QtCore.QRect(51, 402, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB54.setFont(font)
self.USB54.setAutoExclusive(False)
self.USB54.setObjectName(_fromUtf8("USB54"))
self.USB1000 = QtGui.QRadioButton(Dialog)
self.USB1000.setGeometry(QtCore.QRect(51, 315, 59, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB1000.setFont(font)
self.USB1000.setAutoExclusive(False)
self.USB1000.setObjectName(_fromUtf8("USB1000"))
self.USB84 = QtGui.QRadioButton(Dialog)
self.USB84.setGeometry(QtCore.QRect(51, 344, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB84.setFont(font)
self.USB84.setAutoExclusive(False)
self.USB84.setObjectName(_fromUtf8("USB84"))
self.USB69 = QtGui.QRadioButton(Dialog)
self.USB69.setGeometry(QtCore.QRect(51, 373, 41, 23))
font = QtGui.QFont()
font.setPointSize(12)
self.USB69.setFont(font)
self.USB69.setAutoExclusive(False)
self.USB69.setObjectName(_fromUtf8("USB69"))
self.AvailSurveys = QtGui.QListWidget(Dialog)
self.AvailSurveys.setGeometry(QtCore.QRect(21, 35, 256, 192))
self.AvailSurveys.setObjectName(_fromUtf8("AvailSurveys"))
self.TransectCharacteristics = QtGui.QListWidget(Dialog)
self.TransectCharacteristics.setGeometry(
QtCore.QRect(320, 35, 256, 101))
self.TransectCharacteristics.setObjectName(
_fromUtf8("TransectCharacteristics"))
self.DoCalcs = QtGui.QPushButton(Dialog)
self.DoCalcs.setGeometry(QtCore.QRect(190, 610, 91, 41))
self.DoCalcs.setObjectName(_fromUtf8("DoCalcs"))
self.QuitBttn = QtGui.QPushButton(Dialog)
self.QuitBttn.setGeometry(QtCore.QRect(320, 610, 91, 41))
self.QuitBttn.setObjectName(_fromUtf8("QuitBttn"))
self.MinDepthLabel = QtGui.QLabel(Dialog)
self.MinDepthLabel.setGeometry(QtCore.QRect(130, 510, 131, 31))
self.MinDepthLabel.setWordWrap(True)
self.MinDepthLabel.setObjectName(_fromUtf8("MinDepthLabel"))
self.MinDepth = QtGui.QPlainTextEdit(Dialog)
self.MinDepth.setGeometry(QtCore.QRect(20, 510, 101, 31))
self.MinDepth.setObjectName(_fromUtf8("MinDepth"))
self.MaxDepth = QtGui.QPlainTextEdit(Dialog)
self.MaxDepth.setGeometry(QtCore.QRect(310, 510, 101, 31))
self.MaxDepth.setObjectName(_fromUtf8("MaxDepth"))
self.MaxDepthLabel = QtGui.QLabel(Dialog)
self.MaxDepthLabel.setGeometry(QtCore.QRect(420, 510, 131, 31))
self.MaxDepthLabel.setWordWrap(True)
self.MaxDepthLabel.setObjectName(_fromUtf8("MaxDepthLabel"))
self.retranslateUi(Dialog)
QtCore.QMetaObject.connectSlotsByName(Dialog)
def retranslateUi(self, Dialog):
Dialog.setWindowTitle(
_translate("Dialog", "Green Sea Urchin Analysis Program", None))
self.AllSurveys.setText(_translate("Dialog", "Do All Surveys?", None))
self.label.setText(
_translate(
"Dialog",
"<html><head/><body><p align=\"center\"><span style=\" font-size:12pt;\">Survey</span></p></body></html>",
None))
self.label_2.setText(
_translate(
"Dialog",
"<html><head/><body><p align=\"center\"><span style=\" font-size:12pt;\">Transect Characteristics</span></p></body></html>",
None))
self.CalculateAllometric.setText(
_translate(
"Dialog", "Attempt to Estimate\n"
"Allometric Relationship\n"
"from Data?", None))
self.label_4.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:8pt;\">W=exp(alpha+beta*log(L)+epsilon)</span></p><p><span style=\" font-size:8pt;\">log(alpha)~N(mu</span><span style=\" font-size:8pt; vertical-align:sub;\">alpha</span><span style=\" font-size:8pt;\">,sigma</span><span style=\" font-size:8pt; vertical-align:sub;\">alpha</span><span style=\" font-size:8pt; vertical-align:super;\">2</span><span style=\" font-size:8pt;\">) beta~N(mu</span><span style=\" font-size:8pt; vertical-align:sub;\">beta</span><span style=\" font-size:8pt;\">,sigma</span><span style=\" font-size:8pt; vertical-align:sub;\">beta</span><span style=\" font-size:8pt; vertical-align:super;\">2</span><span style=\" font-size:8pt;\">) epsilon~N(0,sigma</span><span style=\" font-size:8pt; vertical-align:sub;\">epsilon</span><span style=\" font-size:8pt; vertical-align:super;\">2</span><span style=\" font-size:8pt;\">)</span></p></body></html>",
None))
self.intcptLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:12pt;\">mu</span><span style=\" font-size:12pt; vertical-align:sub;\">alpha</span></p></body></html>",
None))
self.sdintcptLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:12pt;\">sigma</span><span style=\" font-size:12pt; vertical-align:sub;\">alpha</span></p></body></html>",
None))
self.sigmabetaLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:12pt;\">sigma</span><span style=\" font-size:12pt; vertical-align:sub;\">beta</span></p></body></html>",
None))
self.mubetaLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:12pt;\">mu</span><span style=\" font-size:12pt; vertical-align:sub;\">beta</span></p></body></html>",
None))
self.sigmaepsilonLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:12pt;\">sigma</span><span style=\" font-size:12pt; vertical-align:sub;\">epsilon</span></p></body></html>",
None))
self.groupBox_2.setTitle(
_translate("Dialog", "Upper Size Bounds (mm)", None))
self.NumberBootstrapLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:10pt;\">Number of Bootstrap Repititions</span></p></body></html>",
None))
self.RandomSeedLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:10pt;\">Random Seed</span></p></body></html>",
None))
self.USB39.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB39.setText(_translate("Dialog", "39", None))
self.USB24.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB24.setText(_translate("Dialog", "24", None))
self.USB54.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB54.setText(_translate("Dialog", "54", None))
self.USB1000.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB1000.setText(_translate("Dialog", "1000", None))
self.USB84.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB84.setText(_translate("Dialog", "84", None))
self.USB69.setToolTip(
_translate(
"Dialog",
"<html><head/><body><p align=\"right\"><span style=\" font-size:12pt;\"><br/></span></p></body></html>",
None))
self.USB69.setText(_translate("Dialog", "69", None))
self.DoCalcs.setText(_translate("Dialog", "Do\n" "Calculations", None))
self.QuitBttn.setText(_translate("Dialog", "Quit", None))
self.MinDepthLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:10pt;\">Minimum Depth (m)</span></p></body></html>",
None))
self.MaxDepthLabel.setText(
_translate(
"Dialog",
"<html><head/><body><p><span style=\" font-size:10pt;\">Maximum Depth (m)</span></p></body></html>",
None))
def FillSurveys(self):
self.AS = AllSurveys(self.ODB)
FullName = self.AS.GetCombo()
for fn in FullName:
item = QListWidgetItem(fn)
self.AvailSurveys.addItem(item)
self.AvailSurveys.setSelectionMode(
QtGui.QAbstractItemView.MultiSelection)
def FillTranChar(self):
for fieldname in [
'SurveyTitle', 'SubSampleLocation', 'Year', 'StatArea',
'SubArea'
]:
item = QListWidgetItem(fieldname)
self.TransectCharacteristics.addItem(item)
#pdb.set_trace()
self.TransectCharacteristics.setSelectionMode(
QtGui.QAbstractItemView.MultiSelection)
def MakeConnect(self):
#pdb.set_trace()
self.DoCalcs.clicked.connect(self.Calculations)
self.QuitBttn.clicked.connect(self.QuitCalcs)
self.AllSurveys.stateChanged.connect(self.DoAllSurveys)
self.TransectCharacteristics.itemSelectionChanged.connect(
self.CoordStatAreaSubArea)
def Calculations(self):
print('\nCalculations Started')
seed(int(self.RandomSeed.document().toPlainText()))
self.GetSelectedSurveys()
self.GetSelectedTranChar()
self.GetSelectedUppSizeBound()
self.CalcAllometric = self.CalculateAllometric.isChecked()
self.GetAlloParam()
self.TranClassChar=MetaTransectClass(self.ODB,\
self.SelectedSurveys,\
self.SelectedTranchar,\
CalcAllo=self.CalcAllometric,
DefaultAllo=AlloEqn(intcpt=self.AlloParam['intcpt'],\
sdintcpt=self.AlloParam['sdintcpt'],\
mnbeta=self.AlloParam['mubeta'],\
sdbeta=self.AlloParam['sigmabeta'],\
sigmawithin=self.AlloParam['sigmaepsilon']))
self.PrepOUTmdb()
dictSelectedSurveys = self.SelectedSurveystoDict()
CopyMDB(self.ODB, self.OUTmdb, dictSelectedSurveys)
CB = [99, 95, 90, 75, 50]
nboot = int(self.NumberBootstrap.document().toPlainText())
for i in range(self.TranClassChar.nclass):
FTC = self.TranClassChar.FormatTranClass(i)
if self.TranClassChar.TranClass != [[]]:
print('\nSurveyTitle: ', FTC['SurveyTitle'])
print('SubSampleLocation: ', FTC['SubSampleLocation'])
if FTC['Year'] != MinInt: print('Year: ', FTC['Year'])
if FTC['StatArea'] != MinInt:
print('StatArea: ', FTC['StatArea'])
if FTC['SubArea'] != MinInt:
print('SubArea: ', FTC['SubArea'])
print(len(self.TranClassChar.key[i]), ' transects')
tc=transectclass(self.ODB,self.TranClassChar.key[i],self.TranClassChar.Allo[i],QueryFunc,\
SizeBound=self.UppSizeBnd,\
MinDepth=float(self.MinDepth.document().toPlainText()),\
MaxDepth=float(self.MaxDepth.document().toPlainText()))
CurDeterm = tc.GetFormatEstVal()
CurCB = tc.GetPctCB(CB, nboot=nboot)
#Transect Classes
self.OUTmdb.ADDTo_TranChar(FTC['SurveyTitle'],FTC['SubSampleLocation'],FTC['Year'],FTC['StatArea'],FTC['SubArea'],FTC['InBed'],FTC['NumTran'],\
tc.GetSurveyedArea(),\
tc.GetNumSurveyedQuadInDepthRange(),
tc.AlloSource.intcpt,tc.AlloSource.sdintcpt,\
tc.AlloSource.mnbeta,tc.AlloSource.sdbeta,
tc.AlloSource.sigmawithin)
tck = self.OUTmdb.GetTranCharKey(FTC['SurveyTitle'],
FTC['SubSampleLocation'],
FTC['Year'], FTC['StatArea'],
FTC['SubArea'], FTC['InBed'])
tc.WriteTransectResults(self.OUTmdb, tck)
#The confidence bounds
for cbResult in CurCB:
CBval = cbResult['CB']
SN = list(filter(lambda x: x != 'CB', cbResult.keys()))
for sn in SN:
CurSize = cbResult[sn]
SK = self.OUTmdb.GetSizeRangeKey(CurSize['SizeLimit'][-1])
self.OUTmdb.ADDTo_ConfInterval(\
tck,SK,\
CBval,\
CurSize['linear']['Pop'][0], CurSize['linear']['Pop'][1], \
CurSize['spatial']['Pop'][0], CurSize['spatial']['Pop'][1], \
CurSize['linear']['Bmass'][0], CurSize['linear']['Bmass'][1], \
CurSize['spatial']['Bmass'][0], CurSize['spatial']['Bmass'][1])
#The estimated values
for sn in CurDeterm.keys():
CurSize = CurDeterm[sn]
SK = self.OUTmdb.GetSizeRangeKey(CurSize['SizeLimit'][-1])
self.OUTmdb.ADDTo_EstDens(\
CurSize['linear']['Pop'],CurSize['spatial']['Pop'],\
CurSize['linear']['Bmass'],CurSize['spatial']['Bmass'],\
TranCharKey=tck,SizeKey=SK)
print('\ndone MainWindow Line 274')
def GetAlloParam(self):
#pdb.set_trace()
self.AlloParam = {}
try:
self.AlloParam['intcpt'] = float(
self.intcpt.document().toPlainText())
except:
print('MainWindow 267,type(self.intcpt.document().toPlainText() )',
type(self.intcpt.document().toPlainText()),
self.intcpt.document().toPlainText())
self.AlloParam['intcpt'] = None
try:
self.AlloParam['sdintcpt'] = float(
self.sdintcpt.document().toPlainText())
except:
self.AlloParam['sdintcpt'] = None
try:
self.AlloParam['mubeta'] = float(
self.mubeta.document().toPlainText())
except:
self.AlloParam['mubeta'] = None
try:
self.AlloParam['sigmabeta'] = float(
self.sigmabeta.document().toPlainText())
except:
self.AlloParam['sigmabeta'] = None
try:
self.AlloParam['sigmaepsilon'] = float(
self.sigmaepsilon.document().toPlainText())
except:
self.AlloParam['sigmaepsilon'] = None
def GetSelectedUppSizeBound(self):
self.UppSizeBnd = []
if self.USB24.isChecked(): self.UppSizeBnd += [24]
if self.USB39.isChecked(): self.UppSizeBnd += [39]
if self.USB54.isChecked(): self.UppSizeBnd += [54]
if self.USB69.isChecked(): self.UppSizeBnd += [69]
if self.USB84.isChecked(): self.UppSizeBnd += [84]
self.UppSizeBnd += [inf]
def GetSelectedTranChar(self):
self.SelectedTranchar = []
for index in range(self.TransectCharacteristics.count()):
if self.TransectCharacteristics.item(index).isSelected():
self.SelectedTranchar += [
self.TransectCharacteristics.item(index).text()
]
def GetSelectedSurveys(self):
self.SelectedSurveys = []
year = self.AS.GetYear()
survey = self.AS.GetSurvey()
for index in range(self.AvailSurveys.count()):
if self.AvailSurveys.item(index).isSelected():
self.SelectedSurveys += [[survey[index], year[index]]]
def DoAllSurveys(self):
if self.AllSurveys.isChecked():
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(True)
else:
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(False)
def CoordStatAreaSubArea(self):
'''Make sure statarea and subarea are coherent'''
#Update list of selected transect-characteristics
self.GetSelectedTranChar()
#if subarea is selected, force statarea to be selected
if ('SubArea' in self.SelectedTranchar
) and not ('StatArea' in self.SelectedTranchar):
for index in range(self.TransectCharacteristics.count()):
if self.TransectCharacteristics.item(
index).text() == 'StatArea':
self.TransectCharacteristics.item(index).setSelected(True)
self.GetSelectedTranChar()
def QuitCalcs(self):
print('No Calculations')
sys.exit(app.exec_())
def DefaultSettings(self):
self.intcpt.insertPlainText('-6.8664802585167077')
self.sdintcpt.insertPlainText('0.034723646241811214')
self.mubeta.insertPlainText('2.7276732805478963')
self.sigmabeta.insertPlainText('0.0088232364135380891')
self.sigmaepsilon.insertPlainText('0.15967472910118682')
self.NumberBootstrap.insertPlainText('10000')
self.RandomSeed.insertPlainText('756')
self.MinDepth.insertPlainText('-1000')
self.MaxDepth.insertPlainText('1000')
self.CalculateAllometric.setChecked(True)
self.USB1000.setDisabled(True)
self.USB1000.setChecked(True)
self.USB54.setChecked(True)
self.USB24.autoExclusive = False
def PrepOUTmdb(self):
'''Put information into output. Not the stats - just the metadata'''
self.OUTmdb.ADDTo_Analysis(int(self.NumberBootstrap.document().toPlainText()),\
int(self.RandomSeed.document().toPlainText()),\
float(self.MinDepth.document().toPlainText()),\
float(self.MaxDepth.document().toPlainText()))
self.OUTmdb.ADDTo_SizeRange(0, self.UppSizeBnd[0])
for x in range(1, len(self.UppSizeBnd)):
self.OUTmdb.SizeRangeKey.Increment()
self.OUTmdb.ADDTo_SizeRange(1 + self.UppSizeBnd[x - 1],
self.UppSizeBnd[x])
for sy in self.SelectedSurveys:
self.OUTmdb.ADDTo_SurveyUsed(sy[0], sy[1])
def SelectedSurveystoDict(self):
'''Convert self.SelectedSurveys as a list of dictionaries'''
if isinstance(self.SelectedSurveys[0], dict):
return (self.SelectedSurveys)
result = [{
'SurveyTitle': t[0],
'Year': t[1]
} for t in self.SelectedSurveys]
return (result)
class GeoduckMain(QMainWindow, GeoduckDialog):
def __init__(self, ODB, OUTmdb, parent=None):
self.inMDB = ODB
self.resultODB = OUTmdb
QMainWindow.__init__(self, parent)
self.setupUi(self)
self.MakeConnect()
self.OUTmdb = self.resultODB.ODB
self.ODB = self.inMDB.ODB
self.FillSurveys()
self.DefaultSettings()
self.setFocus()
def MakeConnect(self):
self.DoCalcs.clicked.connect(self.Calculations)
self.QuitBttn.clicked.connect(self.QuitCalcs)
self.AllSurveys.stateChanged.connect(self.DoAllSurveys)
def FillSurveys(self):
self.AS = AllSurveys(self.ODB)
FullName = self.AS.GetCombo()
for fn in FullName:
item = QListWidgetItem(fn)
self.AvailSurveys.addItem(item)
self.AvailSurveys.setSelectionMode(QAbstractItemView.MultiSelection)
def DefaultSettings(self):
self.NumberBootstrap.insertPlainText('10000')
self.RandomSeed.insertPlainText('756')
self.MinDepth.insertPlainText('3')
self.MaxDepth.insertPlainText('1000')
def Calculations(self):
#Do nothing unless some surveys are selected
if self.AvailSurveys.count() == 0: return
try:
self.GetSelectedSurveys()
except:
self.QuitCalcs()
print('\nCalculations Started')
self.TranClassChar=MetaTransectClass(self.ODB,\
self.SelectedSurveys)
CB = [99, 95, 90, 75, 50]
self.Comments = self.RunComments.document().toPlainText()
self.nboot = int(self.NumberBootstrap.document().toPlainText())
self.seed = int(self.RandomSeed.document().toPlainText())
self.LeastDepth = float(self.MinDepth.document().toPlainText())
self.MostDepth = float(self.MaxDepth.document().toPlainText())
AlloSource = QueryFunc.AlloEqn()
SiteSamp = []
SiteEst = []
SampSite = []
TranClass = []
#Beginning of run 2 ###
#Results based on LOBF as a basis for esitmating site-area
print('\nResults based on Line Of Best Fit')
self.OUTmdb.AnalysisKey.Increment()
SiteSamp2 = []
for i in range(self.TranClassChar.nclass):
print("\nSurvey: ", self.TranClassChar.GetChar(i, 'SurveyTitle'))
print("Year: ", self.TranClassChar.GetChar(i, 'Year'))
print("Site:", self.TranClassChar.GetChar(i, 'SurveySite'))
#Random seeds will be manually gernerated for each sample of transects
curseed = self.seed + i * self.nboot
print('Reading Data')
CTC=GDuckTransectclass(self.ODB,i,self.TranClassChar,AlloSource,QueryFunc,\
MinDepth=self.LeastDepth,MaxDepth=self.MostDepth,\
OnlyOnBed=False,curseed=curseed)
TranClass += [CTC]
SiteEst += [{
'ntransect': CTC.ntransect,
'MeanWeight': CTC.MeanWeight,
'SiteSize': CTC.SiteSize
}]
SiteEst[i]['Area'] = SiteEst[i]['SiteSize'].GetEstArea(
Digitized=False)
SiteEst[i]['PopDens'] = CTC.GetAvgAbundance()
SiteEst[i]['Pop'] = SiteEst[i]['Area'] * SiteEst[i]['PopDens']
SiteEst[i]['BiomassDens'] = CTC.GetAvgAbundance(
) * CTC.MeanWeight.EstMeanWeight
SiteEst[i][
'Biomass'] = SiteEst[i]['Area'] * SiteEst[i]['BiomassDens']
print("Number of Transects: ", CTC.ntransect)
print('Writing results for individual transects')
SiteSize = CTC.SiteSize
MeanWeight = CTC.MeanWeight
CTC.WriteTransectResults(self.OUTmdb, RemoveOffBed=False)
SiteSize = CTC.SiteSize
MeanWeight = CTC.MeanWeight
self.OUTmdb.ADDTo_Results_Site(
CTC.site, SiteSize.LOBF,
SiteSize.GetMeanTranLen().mu,
SiteSize.GetEstArea(Digitized=False),
SiteSize.GetSEEstArea(Digitized=False),
MeanWeight.EstMeanWeight / 1000,
MeanWeight.MeanWeightSE / 1000, MeanWeight.MeanWeightSource,
CTC.ntransect, CTC.GetAvgAbundance(),
CTC.GetAvgAbundance() * SiteSize.LOBFarea.mu,
CTC.GetAvgAbundance() * CTC.MeanWeight.EstMeanWeight,
CTC.GetAvgAbundance() * CTC.MeanWeight.EstMeanWeight *
SiteSize.LOBFarea.mu, self.TranClassChar.AnalyzeSite[i])
print('Calculating Confidence Bounds')
Area = CTC.SiteSize.GetRandomArea(n=self.nboot, RunNumber=2)
SiteSamp2+=[CTC. WriteSiteCB(self.OUTmdb,nboot=self.nboot,\
CB=CB,RunNumber=2) ]
print('\nCombined')
#Reduce datasets to sites that should be combined into overall results
SiteEst, SiteSamp2 = SelectGood(self.TranClassChar.AnalyzeSite,
SiteEst), SelectGood(
self.TranClassChar.AnalyzeSite,
SiteSamp2)
self.WriteOverall(SiteEst, SiteSamp2, CB)
SurveyArea = sum(list(map(lambda x: x['Area'], SiteEst)))
ntransect = sum(list(map(lambda x: x['ntransect'], SiteEst)))
self.OUTmdb.ADDTo_Results_Header(self.TranClassChar,2,self.Comments,SurveyArea,\
ntransect,self.nboot,self.seed, self.LeastDepth,self.MostDepth )
#End of run 2 ################
#Beginning of run number 4 #################
dummy = self.OUTmdb.AnalysisKey.GetValue(
IncrementFirst=True) #increment key for sets of analyses
SiteEst = []
for i in range(self.TranClassChar.nclass):
print('\n')
print("Survey: ", self.TranClassChar.GetChar(i, 'SurveyTitle'))
print("Year: ", self.TranClassChar.GetChar(i, 'Year'))
print("Site:", self.TranClassChar.GetChar(i, 'SurveySite'))
print('Reading Data')
CTC = TranClass[i]
CTC.ReduceToOnBed() #CTC.SiteSize is corrected here
print("Number of Transects: ", CTC.ntransect)
print('Writing results for individual transects')
CTC.WriteTransectResults(self.OUTmdb, RemoveOffBed=False)
print('Number of transects onbed: ', CTC.ntransect)
SiteSize = CTC.SiteSize
MeanWeight = CTC.MeanWeight
#Use Digitized Area
print('Writing estimated values - digitized area')
#Later change could use the expectation value for Area.
#Area=SiteSize.DigitizedArea.mu
Area = SiteSize.GetEstArea(Digitized=True)
PopDens = CTC.GetAvgAbundance()
Pop = PopDens * Area
BmaDens = PopDens * CTC.MeanWeight.EstMeanWeight
Bma = Pop * CTC.MeanWeight.EstMeanWeight
if CTC.ntransect <= 0:
PopDens = MinInt
Pop = MinInt
BmaDens = MinInt * 1000
Bma = MinInt * 1000000
###Area=SiteSize.GetDigitizedArea().mu
if Area < 0:
Pop = MinInt
Bma = MinInt * 1000000
self.OUTmdb.ADDTo_Results_Site(
CTC.site,
0, # LOBF is irrelevent for run#4
SiteSize.GetMeanTranLen().mu,
Area,
SiteSize.GetSEEstArea(Digitized=True),
MeanWeight.EstMeanWeight / 1000,
MeanWeight.MeanWeightSE / 1000,
MeanWeight.MeanWeightSource,
CTC.ntransect,
PopDens,
Pop,
BmaDens,
Bma,
self.TranClassChar.AnalyzeSite[i])
SiteEst+=[{'PopDens':PopDens,\
'Pop':Pop,\
'BiomassDens':BmaDens,
'Biomass':Bma,
'Area':Area,\
'ntransect':CTC.ntransect,'MeanWeight':CTC.MeanWeight,'SiteSize':CTC.SiteSize}]
print('Calculating Confidence Bounds')
SiteSamp += [
CTC.WriteSiteCB(self.OUTmdb,
nboot=self.nboot,
CB=CB,
RunNumber=4,
Area=None)
]
print('\nCombined')
#Reduce datasets to sites that should be combined into overall results
SiteEst, SiteSamp2 = SelectGood(self.TranClassChar.AnalyzeSite,
SiteEst), SelectGood(
self.TranClassChar.AnalyzeSite,
SiteSamp2)
self.WriteOverall(SiteEst, SiteSamp, CB)
SurveyArea = sum(list(map(lambda x: x['Area'], SiteEst)))
ntransect = sum(list(map(lambda x: x['ntransect'], SiteEst)))
self.OUTmdb.ADDTo_Results_Header(self.TranClassChar,4,self.Comments,SurveyArea,\
ntransect,self.nboot,self.seed, self.LeastDepth,self.MostDepth )
#End of run 4 ###############
dictSelectedSurveys = self.SelectedSurveystoDict()
CopyMDB(self.ODB, self.OUTmdb, dictSelectedSurveys)
print('\nResults are in ', self.OUTmdb.OUTmdbName)
return
def WriteOverall(self, SiteEst, SiteSamp, CB):
nsite = len(SiteSamp)
#Deterministic Estimates
MinArea = min(list(map(lambda x: ValorMax(x['Area']), SiteEst)))
if MinArea < 0: #There is an undefined area
EstPop = MinInt
EstBma = MinInt * 1000000
Area = MinInt
PopDens = MinInt
BmaDens = MinInt * 1000
else:
EstPop = sum(list(map(lambda x: x['Pop'], SiteEst)))
EstBma = sum(list(map(lambda x: x['Biomass'], SiteEst)))
Area = sum(list(map(lambda x: x['Area'], SiteEst)))
PopDens = EstPop / Area
BmaDens = EstBma / Area
self.OUTmdb.ADDTo_Results_Overall(PopDens, EstPop, BmaDens, EstBma)
#Confidence Bounds
CBoverall = CombineSites(SiteSamp, CB)
for i in range(len(CB)):
self.OUTmdb.ADDTo_Results_OverallConfBounds(CB[i],\
CBoverall['PopDens'][i][1], CBoverall['PopDens'][i][2],\
CBoverall['SitePop'][i][1], CBoverall['SitePop'][i][2],\
CBoverall['BioDens'][i][1], CBoverall['BioDens'][i][2],\
CBoverall['SiteBioM'][i][1], CBoverall['SiteBioM'][i][2])
def GetSelectedSurveys(self):
self.SelectedSurveys = []
year = self.AS.GetYear()
survey = self.AS.GetSurvey()
for index in range(self.AvailSurveys.count()):
if self.AvailSurveys.item(index).isSelected():
self.SelectedSurveys += [[survey[index], year[index]]]
def DoAllSurveys(self):
if self.AllSurveys.isChecked():
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(True)
else:
for index in range(self.AvailSurveys.count()):
self.AvailSurveys.item(index).setSelected(False)
def QuitCalcs(self):
print('\nBye Bye')
os._exit(0)
quit()
sys.exit(app.exec_())
def PrepOUTmdb(self):
'''Put information into output. Not the stats - just the metadata'''
RunNumber = -1
for ss in self.SelectedSurveys:
self.OUTmdb.ADDTo_SurveyUsed(ss[0], str(ss[1]))
def SelectedSurveystoDict(self):
'''Convert self.SelectedSurveys as a list of dictionaries'''
if isinstance(self.SelectedSurveys[0], dict):
return (self.SelectedSurveys)
result = [{
'SurveyTitle': t[0],
'Year': t[1]
} for t in self.SelectedSurveys]
return (result)