def readAproj():
global model, aprojFileName, aprojSaveDir
model = AnimatLabModel.AnimatLabModel(folders.animatlab_rootFolder)
aprojFileName = os.path.split(model.aprojFile)[-1]
aprojSaveDir = folders.animatlab_rootFolder + "AprojFiles/"
if not os.path.exists(aprojSaveDir):
os.makedirs(aprojSaveDir)
copyFileDir(animatsimdir, aprojSaveDir, copy_dir=0)
print "... FINISHED"
except:
if verbose > 2:
print traceback.format_exc()
## This allows the program to utilize multiprocessing functionality for higher efficiency
if __name__ == '__main__':
## This is example code that you can use as the basis for running your own script.
## ===== ===== ===== ===== ===== ===== ===== ===== ===== =====
## EXAMPLE FOR USING AnimatLabModel CLASS
## ===== ===== ===== ===== ===== ===== ===== ===== ===== =====
# This command creates an AnimatLabModel object that will allow you to access the model elements
model = AnimatLabModel.AnimatLabModel(
"F:/__DISSERTATION/SimulationFiles/_MASTER/FinalDissertationModel/")
## You can see other available methods by typing: model. + <tab>
# See where the .asim XML file is saved -- this is the file that is loaded to generate the AnimatLab model object
#model.asimFile
# To find an element by its name:
#PhasicDepMN = model.getElementByName("Phasic Dep MN")
# To find elements by type:
# Options are: Neurons, Adapters, ExternalStimuli
#Neurons = model.getElementByType("Neurons")
# To find elements by ID:
#TonicLevMN = model.getElementByID("reallycomplicatedidhere")
# ============================================================================
# MAIN PROGRAM
# ============================================================================
if __name__ == '__main__':
"""
"""
sims = AnimatLabSimRunner.AnimatLabSimulationRunner(
"Test Sims",
rootFolder=folders.animatlab_rootFolder,
commonFiles=folders.animatlab_commonFiles_dir,
sourceFiles=folders.python27_source_dir,
simFiles=folders.animatlab_simFiles_dir,
resultFiles=folders.animatlab_result_dir)
model = AnimatLabModel.AnimatLabModel(folders.animatlab_commonFiles_dir)
projMan = ProjectManager.ProjectManager('Test Project')
aprojFileName = os.path.split(model.aprojFile)[-1]
optSet = OptimizeSimSettings(folders=folders,
model=model,
projMan=projMan,
sims=sims)
print
listparNameOpt = optSet.paramLoebName
setPlaybackControlMode(model, mode=0)
# Looks for a parameter file in the chosen directory
fileName = 'paramOpt.pkl'
if loadParams(folders.animatlab_result_dir + fileName, optSet):
listparNameOpt = optSet.paramLoebName
listparValOpt = optSet.paramLoebValue
listparTypeOpt = optSet.paramLoebType
def browse_folder(self):
global folders, sims, model, projman, optSet
# self.listWidget.clear() # If there are any elements in the list
mydir = "//Mac/Home/Documents/Labo/Scripts/AnimatLabV2/Human/test/"
dirname = QtGui.QFileDialog.getExistingDirectory(
self, "Pick a folder", mydir)
# execute getExistingDirectory dialog and set the directory variable
# to be equal to the user selected directory
if dirname: # if user didn't pick a directory don't continue
print "You chose %s" % dirname
subdir = os.path.split(dirname)[-1]
print subdir
folders = FolderOrg(subdir=subdir)
folders.affectDirectories()
saveAnimatLabDir(dirname)
# ################################################################
# Creation of sims & initialisation #
# ################################################################
# Initializes the AnimatLabSimRunner
sims = AnimatLabSimRunner.AnimatLabSimulationRunner(
"Test Sims",
rootFolder=folders.animatlab_rootFolder,
commonFiles=folders.animatlab_commonFiles_dir,
sourceFiles=folders.python27_source_dir,
simFiles=folders.animatlab_simFiles_dir,
resultFiles=folders.animatlab_result_dir)
model = AnimatLabModel.AnimatLabModel(
folders.animatlab_commonFiles_dir)
projMan = ProjectManager.ProjectManager('Test Project')
optSet = OptimizeSimSettings(folders=folders,
model=model,
projMan=projMan,
sims=sims)
# ################################################################
# Default parameters #
# ################################################################
# Parameters for optimization
listparNameOpt = [
'mvtcolumn', 'startMvt1', 'endMvt1', 'endPos1', 'angle1',
'startMvt2', 'endMvt2', 'endPos2', 'angle2', 'startEQM',
'endEQM', 'allstim', 'disabledStimNbs', 'dontChangeStimNbs',
'seriesStimParam', 'allsyn', 'disabledSynNbs',
'dontChangeSynNbs', 'disabledSynFRNbs', 'dontChangeSynFRNbs',
'seriesSynParam', 'seriesSynFRParam', 'nbepoch',
'nbstimtrials', 'nbsyntrials', 'nbsteps', 'deltaStimCoeff',
'maxDeltaStim', 'multSynCoeff', 'maxMultSyn',
'coactivityFactor', 'activThr', 'limQuality', 'maxStim',
'maxSynAmp', 'maxG', 'maxWeight', 'defaultval', 'cmaes_sigma',
'fourchetteStim', 'fourchetteSyn'
]
listparValOpt = [
6, 0, 0.3, 5, 0, 5, 5.8, 10, 60, 3, 10, 1, [], [],
['CurrentOn', 'StartTime', 'EndTime'], 1, [], [], [], [],
['G'], ['Weight'], 2, 1, 1, 4, 1.5, 50, 1.5, 50, 1000, -0.06,
0.0001, 2e-08, 50, 10, 5e-07, 100000.0, 0.0035, 5, 5
]
listparTypeOpt = [
int, float, float, float, float, float, float, float, float,
float, float, int, list, list, list, int, list, list, list,
list, list, list, int, int, int, int, float, float, float,
float, float, float, float, float, float, float, float, float,
float, float, float
]
listparCoulOpt = [
'magenta', 'lightyellow', 'lightyellow', 'lightyellow',
'lightyellow', 'lightyellow', 'lightyellow', 'lightyellow',
'lightyellow', 'lightyellow', 'lightyellow', 'lightblue',
'lightblue', 'lightblue', 'lightblue', 'lightgreen',
'lightgreen', 'lightgreen', 'lightgreen', 'lightgreen',
'lightgreen', 'lightgreen', 'pink', 'pink', 'pink', 'pink',
'pink', 'pink', 'pink', 'pink', 'pink', 'pink', 'pink',
'MistyRose', 'MistyRose', 'MistyRose', 'MistyRose',
'lightPink', 'lightgray', 'lightgray', 'lightgray'
]
# Parameters for Marquez procedure
listparNameMarquez = [
'startTest', 'startTwitch', 'endTwitch', 'endTest',
'twitStMusclesStNbs', 'sensoryNeuronNbs', 'motorNeuronNbs',
'sensoryNeuronFRNbs', 'motorNeuronFRNbs', 'sensColChartNbs',
'mnColChartNbs', 'nbruns', 'timeMes', 'delay', 'eta'
]
listparValMarquez = [
0., 5., 5.1, 8., [0, 1], [], [], [], [], [], [], 3, 0.08, 0.02,
1000
]
listparTypeMarquez = [
float, float, float, float, list, list, list, list, list, list,
list, int, float, float, float
]
listparCoulMarquez = [
'orange', 'orange', 'orange', 'orange', 'orange', 'orange',
'orange', 'orange', 'orange', 'orange', 'orange', 'orange',
'orange', 'orange', 'orange'
]
# ###############################################################
# Looks for a parameter file in the chosen directory #
# ###############################################################
fileName = 'paramOpt.pkl'
if self.loadParams(folders.animatlab_result_dir + fileName, optSet,
listparNameOpt):
listparNameOpt = optSet.paramLoebName
listparValOpt = optSet.paramLoebValue
listparTypeOpt = optSet.paramLoebType
listparCoulOpt = optSet.paramLoebCoul
optSet.actualizeparamLoeb()
listparNameMarquez = optSet.paramMarquezName
listparValMarquez = optSet.paramMarquezValue
listparTypeMarquez = optSet.paramMarquezType
listparCoulMarquez = optSet.paramMarquezCoul
optSet.actualizeparamMarquez()
else:
optSet.paramLoebName = listparNameOpt
optSet.paramLoebValue = listparValOpt
optSet.paramLoebType = listparTypeOpt
optSet.paramLoebCoul = listparCoulOpt
optSet.actualizeparamLoeb()
optSet.paramMarquezName = listparNameMarquez
optSet.paramMarquezValue = listparValMarquez
optSet.paramMarquezType = listparTypeMarquez
optSet.paramMarquezCoul = listparCoulMarquez
optSet.actualizeparamMarquez()
# If no parameter file found, then uses the default parameters
self.exConn = []
for i in range(optSet.nbConnexions):
if optSet.tab_connexions[i][6] == "Disabled" or \
optSet.tab_connexions[i][7] == "Disabled":
self.exConn.append(i)
# print optSet.tab_connexions[i][6]
# print optSet.tab_connexions[i][7]
for i in self.exConn:
if i not in optSet.paramOpt['disabledSynNbs']:
optSet.paramOpt['disabledSynNbs'].append(i)
# optSet.paramOpt['disabledSynNbs'] += self.exConn
optSet.paramOpt['disabledSynNbs'] = \
list(set(optSet.paramOpt['disabledSynNbs']))
optSet.disabledSynNames = []
for i in optSet.disabledSynNbs:
optSet.disabledSynNames.append(optSet.connexName[i])
self.exConnFR = []
for i in range(optSet.nbSynapsesFR):
if optSet.tab_connexionsFR[i][3] == "Disabled" or \
optSet.tab_connexionsFR[i][4] == "Disabled":
self.exConnFR.append(i)
for i in self.exConnFR:
if i not in optSet.paramOpt['disabledSynFRNbs']:
optSet.paramOpt['disabledSynFRNbs'].append(i)
# optSet.paramOpt['disabledSynFRNbs'] += self.exConnFR
optSet.paramOpt['disabledSynFRNbs'] = \
list(set(optSet.paramOpt['disabledSynFRNbs']))
optSet.disabledSynFRNames = []
for i in optSet.disabledSynFRNbs:
optSet.disabledSynFRNames.append(optSet.connexFRName[i])
self.exStim = []
for i in range(optSet.nbStims):
name = optSet.model.getElementByID(optSet.tab_stims[i][6]).\
find('Name').text
# print name
if name == "Disabled":
self.exStim.append(i)
for i in self.exStim:
if i not in optSet.paramOpt['disabledStimNbs']:
optSet.paramOpt['disabledStimNbs'].append(i)
# optSet.paramOpt['disabledStimNbs'] += self.exStim
optSet.paramOpt['disabledStimNbs'] = \
list(set(optSet.paramOpt['disabledStimNbs']))
optSet.disabledStimNames = []
for i in optSet.disabledStimNbs:
optSet.disabledStimNames.append(optSet.stimName[i])
for i in range(len(self.exStim)):
self.exStimName.append(optSet.stimName[self.exStim[i]])
for i in range(len(self.exConn)):
self.exConnName.append(optSet.connexName[self.exConn[i]])
for i in range(len(self.exConnFR)):
self.exConnFRName.append(optSet.connexFRName[self.exConnFR[i]])
# ################################################################
# Select list of External Stimuli #
# ################################################################
self.tableWidget.setRowCount(len(optSet.stimName))
self.tableWidget.setColumnCount(2)
self.tableWidget.verticalHeader().hide()
self.tableWidget.horizontalHeader().hide()
for i in range(len(optSet.stimName)):
itm1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.stimName[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['dontChangeStimNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['disabledStimNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget.setItem(i, 0, itm1)
self.tableWidget.setItem(i, 1, itm2)
self.tableWidget.item(i, 0).\
setBackground(QtGui.QColor(optSet.paramLoebCoul[11]))
self.tableWidget.resizeColumnsToContents()
self.tableWidget.cellClicked.connect(self.stim_cell_was_clicked)
# ################################################################
# Select list of Connexions #
# ################################################################
self.tableWidget_2.setRowCount(len(optSet.connexName))
self.tableWidget_2.setColumnCount(2)
self.tableWidget_2.verticalHeader().hide()
self.tableWidget_2.horizontalHeader().hide()
for i in range(len(optSet.connexName)):
itm1 = QtGui.\
QTableWidgetItem("{0} {1}".
format(i, optSet.connexName[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['dontChangeSynNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['disabledSynNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_2.setItem(i, 0, itm1)
self.tableWidget_2.setItem(i, 1, itm2)
self.tableWidget_2.item(i, 0).\
setBackground(QtGui.QColor(optSet.paramLoebCoul[15]))
self.tableWidget_2.resizeColumnsToContents()
self.tableWidget_2.cellClicked.connect(self.connex_cell_was_clicked)
# self.tableWidget_2.setColumnWidth(0, 80)
# self.tableWidget_2.horizontalHeader().setDefaultSectionSize(140)
# self.tableWidget_2.verticalHeader().setStretchLastSection(True)
# ################################################################
# Select list of ConnexionsFR #
# ################################################################
self.tableWidget_3.setRowCount(len(optSet.connexFRName))
self.tableWidget_3.setColumnCount(2)
self.tableWidget_3.verticalHeader().hide()
self.tableWidget_3.horizontalHeader().hide()
for i in range(len(optSet.connexFRName)):
itm1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.connexFRName[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['dontChangeSynFRNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramOpt['disabledSynFRNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_3.setItem(i, 0, itm1)
self.tableWidget_3.setItem(i, 1, itm2)
self.tableWidget_3.item(i, 0).\
setBackground(QtGui.QColor(optSet.paramLoebCoul[15]))
self.tableWidget_3.resizeColumnsToContents()
self.tableWidget_3.cellClicked.connect(self.connexFR_cell_was_clicked)
# self.tableWidget_3.setColumnWidth(0, 80)
# self.tableWidget_3.horizontalHeader().setDefaultSectionSize(140)
# self.tableWidget_3.horizontalHeader().setStretchLastSection(True)
# ################################################################
# Select list of Neurons #
# ################################################################
self.tableWidget_4.setRowCount(len(optSet.neuronNames))
self.tableWidget_4.setColumnCount(2)
self.tableWidget_4.verticalHeader().hide()
self.tableWidget_4.horizontalHeader().hide()
for i in range(len(optSet.neuronNames)):
itm1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.neuronNames[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['sensoryNeuronNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['motorNeuronNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_4.setItem(i, 0, itm1)
self.tableWidget_4.setItem(i, 1, itm2)
self.tableWidget_4.item(i, 0).\
setBackground(QtGui.QColor('gold'))
self.tableWidget_4.resizeColumnsToContents()
self.tableWidget_4.cellClicked.connect(self.neuron_cell_was_clicked)
# ################################################################
# Select list of NeuronsFR #
# ################################################################
self.tableWidget_5.setRowCount(len(optSet.neuronFRNames))
self.tableWidget_5.setColumnCount(2)
self.tableWidget_5.verticalHeader().hide()
self.tableWidget_5.horizontalHeader().hide()
for i in range(len(optSet.neuronFRNames)):
itm1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.neuronFRNames[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['sensoryNeuronFRNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['motorNeuronFRNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_5.setItem(i, 0, itm1)
self.tableWidget_5.setItem(i, 1, itm2)
self.tableWidget_5.item(i, 0).\
setBackground(QtGui.QColor('gold'))
self.tableWidget_5.resizeColumnsToContents()
self.tableWidget_5.cellClicked.connect(self.neuronFR_cell_was_clicked)
# ################################################################
# Select list of Chart Names #
# ################################################################
self.tableWidget_6.setRowCount(len(optSet.chartColNames))
self.tableWidget_6.setColumnCount(3)
self.tableWidget_6.verticalHeader().hide()
self.tableWidget_6.horizontalHeader().hide()
for i in range(len(optSet.chartColNames)):
itm1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.chartColNames[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['sensColChartNbs']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
itm2 = QtGui.QTableWidgetItem("")
itm2.setFlags(itm2.flags() | QtCore.Qt.ItemIsUserCheckable)
if i in (optSet.paramMarquez['mnColChartNbs']):
itm2.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('blue'))
else:
itm2.setCheckState(QtCore.Qt.Unchecked)
itm3 = QtGui.QTableWidgetItem("")
itm3.setFlags(itm3.flags() | QtCore.Qt.ItemIsUserCheckable)
if i == optSet.paramOpt['mvtcolumn']:
itm3.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('magenta'))
else:
itm3.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_6.setItem(i, 0, itm1)
self.tableWidget_6.setItem(i, 1, itm2)
self.tableWidget_6.setItem(i, 2, itm3)
self.tableWidget_6.item(i, 0).\
setBackground(QtGui.QColor('LavenderBlush'))
self.tableWidget_6.resizeColumnsToContents()
self.tableWidget_6.cellClicked.connect(self.chart_cell_was_clicked)
# ################################################################
# Parameters for Loeb Optimization #
# ################################################################
self.tableWidget_7.setRowCount(len(optSet.paramLoebName))
self.tableWidget_7.setColumnCount(2)
self.tableWidget_7.verticalHeader().hide()
self.tableWidget_7.horizontalHeader().hide()
for i in range(len(optSet.paramLoebName)):
item1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.paramLoebName[i]))
item1.setTextAlignment(QtCore.Qt.AlignRight)
item2 = QtGui.QTableWidgetItem("{0}".format(
optSet.paramLoebValue[i]))
item2.setSizeHint(QSize(500, 0))
self.tableWidget_7.setItem(i, 0, item1)
self.tableWidget_7.setItem(i, 1, item2)
self.tableWidget_7.item(i, 0).\
setBackground(QtGui.QColor(optSet.paramLoebCoul[i]))
self.tableWidget_7.resizeColumnsToContents()
# ################################################################
# Parameters for Marquez Optimization #
# ################################################################
self.tableWidget_8.setRowCount(len(optSet.paramMarquezName))
self.tableWidget_8.setColumnCount(2)
self.tableWidget_8.verticalHeader().hide()
self.tableWidget_8.horizontalHeader().hide()
for i in range(len(optSet.paramMarquezName)):
item1 = QtGui.QTableWidgetItem("{0} {1}".format(
i, optSet.paramMarquezName[i]))
item2 = QtGui.QTableWidgetItem("{0}".format(
optSet.paramMarquezValue[i]))
item2.setSizeHint(QSize(500, 0))
self.tableWidget_8.setItem(i, 0, item1)
self.tableWidget_8.setItem(i, 1, item2)
self.tableWidget_8.item(i, 0).\
setBackground(QtGui.QColor(optSet.paramMarquezCoul[i]))
self.tableWidget_8.resizeColumnsToContents()
# ################################################################
# Select External Stimuli parameters #
# ################################################################
self.tableWidget_9.setRowCount(len(optSet.stimParam))
self.tableWidget_9.setColumnCount(1)
self.tableWidget_9.verticalHeader().hide()
self.tableWidget_9.horizontalHeader().hide()
for i in range(len(optSet.stimParam)):
itm1 = QtGui.QTableWidgetItem(str(optSet.stimParam[i]))
itm1.setFlags(itm1.flags() | QtCore.Qt.ItemIsUserCheckable)
if optSet.stimParam[i] in (optSet.paramOpt['seriesStimParam']):
itm1.setCheckState(QtCore.Qt.Checked)
itm1.setForeground(QtGui.QColor('red'))
else:
itm1.setCheckState(QtCore.Qt.Unchecked)
self.tableWidget_9.setItem(i, 0, itm1)
self.tableWidget_9.item(i, 0).\
setBackground(QtGui.QColor('lightCyan'))
self.tableWidget_9.resizeColumnsToContents()
self.tableWidget_9.cellClicked.connect(self.stimPar_cell_was_clicked)