class Walker(object):
def __init__(self):
self.position = PVector(width / 2, height / 2)
self.history = ArrayList()
def display(self):
stroke(0)
fill(175)
rectMode(CENTER)
rect(self.position.x, self.position.y, 16, 16)
beginShape()
stroke(0)
noFill()
for v in self.history:
vertex(v.x, v.y)
endShape()
# Randomly move up, down, left, right, or stay in one place
def walk(self):
vel = PVector(int(random(-2, 2)), int(random(-2, 2)))
self.position.add(vel)
print(self.position)
# Stay on the screen
self.position.x = constrain(self.position.x, 0, width - 1)
self.position.y = constrain(self.position.y, 0, height - 1)
self.history.add(self.position.get())
# print(self.history)
if self.history.size() > 1000:
self.history.remove(0)
def ensureSIFTFeatures(filepath,
paramsSIFT,
properties,
csvDir,
validateByFileExists=False):
"""
filepath: to the image from which SIFT features have been or have to be extracted.
params: dict of registration parameters, including the key "scale".
paramsSIFT: FloatArray2DSIFT.Params instance.
csvDir: directory into which serialized features have been or will be saved.
load: function to load an image as an ImageProcessor from the filepath.
validateByFileExists: whether to merely check that the .obj file exists as a quick form of validation.
First check if serialized features exist for the image, and if the Params match.
Otherwise extract the features and store them serialized.
Returns the ArrayList of Feature instances.
"""
path = os.path.join(csvDir,
os.path.basename(filepath) + ".SIFT-features.obj")
if validateByFileExists:
if os.path.exists(path):
return True
# An ArrayList whose last element is a mpicbg.imagefeatures.FloatArray2DSIFT.Param
# and all other elements are mpicbg.imagefeatures.Feature
features = deserialize(path) if os.path.exists(path) else None
if features:
if features.get(features.size() - 1).equals(paramsSIFT):
features.remove(features.size() - 1) # removes the Params
syncPrintQ("Loaded %i SIFT features for %s" %
(features.size(), os.path.basename(filepath)))
return features
else:
# Remove the file: paramsSIFT have changed
os.remove(path)
# Else, extract de novo:
try:
# Extract features
imp = loadImp(filepath)
ip = imp.getProcessor()
paramsSIFT = paramsSIFT.clone()
ijSIFT = SIFT(FloatArray2DSIFT(paramsSIFT))
features = ArrayList() # of Feature instances
ijSIFT.extractFeatures(ip, features)
ip = None
imp.flush()
imp = None
features.add(
paramsSIFT
) # append Params instance at the end for future validation
serialize(features, path)
features.remove(features.size() -
1) # to return without the Params for immediate use
syncPrintQ("Extracted %i SIFT features for %s" %
(features.size(), os.path.basename(filepath)))
except:
printException()
return features
def create(cls, conjunct, functionInfo, rightmostVar, varOrder, preassignment):
""" generated source for method create """
# We have to set up the things mentioned above...
internalFunctions = ArrayList()
# We can traverse the conjunct for the list of variables/constants...
terms = ArrayList()
gatherVars(conjunct.getBody(), terms)
# Note that we assume here that the var of interest only
# appears once in the relation...
varIndex = terms.indexOf(rightmostVar)
if varIndex == -1:
print "conjunct is: " + conjunct
print "terms are: " + terms
print "righmostVar is: " + rightmostVar
terms.remove(rightmostVar)
function_ = functionInfo.getValueMap(varIndex)
# Set up inputs and such, using terms
querySize = len(terms)
isInputConstant = ArrayList(len(terms))
queryConstants = Maps.newHashMap()
queryInputIndices = ArrayList(len(terms))
i = 0
while i < len(terms):
if isinstance(term, (GdlConstant, )):
isInputConstant.add(True)
queryConstants.put(i, term)
queryInputIndices.add(-1)
elif isinstance(term, (GdlVariable, )):
# Is it in the head assignment?
if preassignment.containsKey(term):
isInputConstant.add(True)
queryConstants.put(i, preassignment.get(term))
queryInputIndices.add(-1)
else:
isInputConstant.add(False)
# queryConstants.add(null);
# What value do we put here?
# We want to grab some value out of the
# input tuple, which uses functional ordering
# Index of the relevant variable, by the
# assignment's ordering
queryInputIndices.add(varOrder.indexOf(term))
i += 1
return AssignmentFunction(ImmutableList.copyOf(internalFunctions), querySize, ImmutableList.copyOf(isInputConstant), ImmutableMap.copyOf(queryConstants), ImmutableList.copyOf(queryInputIndices), ImmutableMap.copyOf(function_))
def getAvailMethodsUser(self, user, skip):
methods = ArrayList()
for method in self.authenticators:
try:
module = self.authenticators[method]
if module.hasEnrollments(module.configAttrs, user):
methods.add(method)
except:
print "Casa. getAvailMethodsUser. hasEnrollments call could not be issued for %s module" % method
try:
#skip is guaranteed to be a member of methods (if hasEnrollments routines are properly implemented).
#A call to remove strangely crashes if skip is absent
methods.remove(skip)
except:
print "Casa. getAvailMethodsUser. methods list does not contain %s" % skip
print "Casa. getAvailMethodsUser %s" % methods.toString()
return methods
class Walker(object):
def __init__(self):
self.position = PVector(width/2, height/2)
self.velocity = PVector()
self.acceleration = PVector()
self.history = ArrayList()
self.noff = PVector(random(1000), random(1000))
def display(self):
stroke(0)
fill(175)
rectMode(CENTER)
rect(self.position.x, self.position.y, 16, 16)
beginShape()
stroke(0)
noFill()
for v in self.history:
vertex(v.x, v.y)
endShape()
# Randomly move up, down, left, right, or stay in one place
def walk(self):
self.acceleration.x = map(noise(self.noff.x), 0, 1, -1, 1)
self.acceleration.y = map(noise(self.noff.y), 0, 1, -1, 1)
self.acceleration.mult(0.1) # Multiply a vector by a scalar
self.noff.add(0.01, 0.01, 0)
self.velocity.add(self.acceleration)
self.velocity.limit(1) # Limit the magnitude of the vector
self.position.add(self.velocity)
self.history.add(self.position.get())
if self.history.size() > 1000 :
self.history.remove(0)
# Stay on the screen
self.position.x = constrain(self.position.x, 0, width-1)
self.position.y = constrain(self.position.y, 0, height-1)
def test_remove(self):
# Verifies that overloaded java.util.List#remove(int) method can still be used, but with Python index semantics
# http://bugs.jython.org/issue2456
jl = ArrayList(xrange(10, -1, -1)) # 10 .. 0, inclusive
jl.remove(0) # removes jl[-1] (=0)
self.assertEqual(jl, range(10, 0, -1)) # 10 .. 1
self.assertRaises(ValueError, jl.remove, Integer(0)) # j.l.Integer does not support __index__ - maybe it should!
jl.remove(0) # removes jl[0] (=10)
self.assertEqual(jl, range(9, 0, -1)) # 9 .. 1
jl.remove(-1) # removes jl[-1] (=1) - support same index calculations as Python (= del jl[-1])
self.assertEqual(jl, range(9, 1, -1)) # 9 .. 2
jl.remove(3)
jl.remove(5)
self.assertEqual(jl, [9, 8, 7, 6, 4, 2])
a_to_z = list(chr(i) for i in xrange(ord('a'), ord('z') + 1))
b_to_z_by_2 = list(chr(i) for i in xrange(ord('b'), ord('z') + 1, 2))
jl = ArrayList(a_to_z)
for i in xrange(13):
jl.remove(i)
self.assertEqual(jl, b_to_z_by_2)
def test_remove(self):
# Verifies that overloaded java.util.List#remove(int) method can still be used, but with Python index semantics
# http://bugs.jython.org/issue2456
jl = ArrayList(xrange(10, -1, -1)) # 10 .. 0, inclusive
jl.remove(0) # removes jl[-1] (=0)
self.assertEqual(jl, range(10, 0, -1)) # 10 .. 1
self.assertRaises(ValueError, jl.remove, Integer(0)) # j.l.Integer does not support __index__ - maybe it should!
jl.remove(0) # removes jl[0] (=10)
self.assertEqual(jl, range(9, 0, -1)) # 9 .. 1
jl.remove(-1) # removes jl[-1] (=1) - support same index calculations as Python (= del jl[-1])
self.assertEqual(jl, range(9, 1, -1)) # 9 .. 2
jl.remove(3)
jl.remove(5)
self.assertEqual(jl, [9, 8, 7, 6, 4, 2])
a_to_z = list(chr(i) for i in xrange(ord('a'), ord('z') + 1))
b_to_z_by_2 = list(chr(i) for i in xrange(ord('b'), ord('z') + 1, 2))
jl = ArrayList(a_to_z)
for i in xrange(13):
jl.remove(i)
self.assertEqual(jl, b_to_z_by_2)
time.sleep(2)
myProject.neuronFileManager.setSuggestedRemoteRunTime(10)
myProject.neuronFileManager.generateTheNeuronFiles(simConfig, None, NeuronFileManager.RUN_HOC, randomseed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
time.sleep(2) # wait for the process to be sent out
simInputs.remove("backgroundExc")
#####################'''
######## Rerunning the same configuration + background exc1500 /inh150% ###############
simInputs.add("backgroundExc")
simInputs.add("backgroundInh150")
simInputs.add("NGF")
simConfig.setInputs(simInputs)
print "group generated: "+simConfig.getCellGroups().toString()
print "going to stimulate: "+simConfig.getInputs().toString()
def getLimitQueryWithout(self, fq):
limits = ArrayList(self.__fqParts)
limits.remove("category/" + fq)
if limits.isEmpty():
return ""
return "/".join(limits)
# importing and using a java array list in jython code import java.util.ArrayList as ArrayList aList = ArrayList() aList.add(10) aList.add(20) print(aList, type(aList)) aList.add(30) aList.remove(20) print(aList)
time.sleep(2)
myProject.neuronFileManager.setSuggestedRemoteRunTime(10)
myProject.neuronFileManager.generateTheNeuronFiles(simConfig, None, NeuronFileManager.RUN_HOC, randomseed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
time.sleep(2) # wait for the process to be sent out
simInputs.remove("backgroundExc")
#####################'''
'''##### Rerunning the same configuration + background exc/inh #####
simRef = prefix+"syn"+str(synapses)+"E1500I43_"+str(t)
print "Simref: "+simRef
myProject.simulationParameters.setReference(simRef)
refStored.append(simRef)
##### RUN BLOCK background exc/inh #####
simInputs.add("backgroundExc")
simInputs.add("backgroundInh")
simConfig.setInputs(simInputs)
def getLimitQueryWithout(self, fq):
limits = ArrayList(self.__fqParts)
limits.remove("category/" + fq)
if limits.isEmpty():
return ""
return "/".join(limits)
time.sleep(2)
myProject.neuronFileManager.setSuggestedRemoteRunTime(10)
myProject.neuronFileManager.generateTheNeuronFiles(simConfig, None, NeuronFileManager.RUN_HOC, randomseed)
print "Generated NEURON files for: "+simRef
compileProcess = ProcessManager(myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0,0)
print "Compiled NEURON files for: "+simRef
if compileSuccess:
pm.doRunNeuron(simConfig)
print "Set running simulation: "+simRef
time.sleep(30) # Wait for sim to be kicked off
simInputs.remove("backgroundExc")
#####################'''
######## Rerunning the same configuration + background exc 1200 ###############
simInputs.add("backgroundExc1200")
simConfig.setInputs(simInputs)
print "group generated: "+simConfig.getCellGroups().toString()
print "going to stimulate: "+simConfig.getInputs().toString()
print "going to record: "+simConfig.getPlots().toString()
##########################################################################################
print("tup1[0]: ", tup1[0])
# Jython Dictionary
dict = {'011': 'New Delhi', '022': 'Mumbai', '033': 'Kolkata', 'Age': 25}
print("dict['011']: ", dict['011'])
print("dict['Age']: ", dict['Age'])
########################################################################################################################
import java.util.ArrayList as ArrayList
arr = ArrayList()
arr.add(10)
arr.add(20)
print("ArrayList: ", arr)
arr.remove(10) #remove 10 from arraylist
arr.add(0, 5) #add 5 at 0th index
print("ArrayList: ", arr)
print("element at index 1:", arr.get(1)) #retrieve item at index 1
arr.set(0,100) #set item at 0th index to 100
print("ArrayList: ", arr)
# Jarray Class
from jarray import array
my_seq = (1, 2, 3, 4, 5)
arr1 = array(my_seq, 'i')
print(arr1)
myStr = "Hello Jython"
arr2 = array(myStr, 'c')
print(arr2)
class GuiLog(AbstractTableModel):
'''
Acts as an AbstractTableModel for the table that is shown in the UI tab:
when this data structure changes, the in-UI table is updated.
'''
def __init__(self, callbacks):
'''
Creates a Java-style ArrayList to hold LogEntries that appear in the table
'''
self.ui = None
self._log = ArrayList()
self._lock = Lock()
self._callbacks = callbacks
self._helpers = callbacks.getHelpers()
def clear(self):
'''
Clears all entries from the table
'''
self._lock.acquire()
last = self._log.size()
if last > 0:
self._log.clear()
self.fireTableRowsDeleted(0, last-1)
# Note: if callees modify table this could deadlock
self._lock.release()
def add_entry(self, entry):
'''
Adds entry to the table
'''
self._lock.acquire()
row = self._log.size()
self._log.add(entry)
# Note: if callees modify table this could deadlock
self.fireTableRowsInserted(row, row)
self._lock.release()
def remove_entry(self, entry):
'''
Removes entry from the table
'''
self._lock.acquire()
for i in range(0, len(self._log)):
ei = self._log[i]
if ei.md5 == entry.md5:
self._log.remove(i)
break
self.fireTableRowsDeleted(i, i)
self._lock.release()
def getRowCount(self):
'''
Used by the Java Swing UI
'''
try:
return self._log.size()
except:
return 0
def getColumnCount(self):
'''
Used by the Java Swing UI
'''
return 5
def getColumnName(self, columnIndex):
'''
Used by the Java Swing UI
'''
cols = ["Time added",
"Tool",
"URL",
"Issue",
"Who"]
try:
return cols[columnIndex]
except KeyError:
return ""
def get(self, rowIndex):
'''
Gets the LogEntry at rowIndex
'''
return self._log.get(rowIndex)
def getValueAt(self, rowIndex, columnIndex):
'''
Used by the Java Swing UI
'''
logEntry = self._log.get(rowIndex)
if columnIndex == 0:
return logEntry.timestamp
elif columnIndex == 1:
return logEntry.tool.capitalize()
elif columnIndex == 2:
return logEntry.url
elif columnIndex == 3:
if logEntry.tool == "scanner":
return logEntry.issue_name
else:
return "N/A"
elif columnIndex == 4:
return logEntry.who
return ""
class GuiLog(AbstractTableModel):
'''
Acts as an AbstractTableModel for the table that is shown in the UI tab:
when this data structure changes, the in-UI table is updated.
'''
def __init__(self, callbacks):
'''
Creates a Java-style ArrayList to hold LogEntries that appear in the table
'''
self.ui = None
self._log = ArrayList()
self._lock = Lock()
self._callbacks = callbacks
self._helpers = callbacks.getHelpers()
def clear(self):
'''
Clears all entries from the table
'''
self._lock.acquire()
last = self._log.size()
if last > 0:
self._log.clear()
self.fireTableRowsDeleted(0, last - 1)
# Note: if callees modify table this could deadlock
self._lock.release()
def add_entry(self, entry):
'''
Adds entry to the table
'''
self._lock.acquire()
row = self._log.size()
self._log.add(entry)
# Note: if callees modify table this could deadlock
self.fireTableRowsInserted(row, row)
self._lock.release()
def remove_entry(self, entry):
'''
Removes entry from the table
'''
self._lock.acquire()
for i in range(0, len(self._log)):
ei = self._log[i]
if ei.md5 == entry.md5:
self._log.remove(i)
break
self.fireTableRowsDeleted(i, i)
self._lock.release()
def getRowCount(self):
'''
Used by the Java Swing UI
'''
try:
return self._log.size()
except:
return 0
def getColumnCount(self):
'''
Used by the Java Swing UI
'''
return 5
def getColumnName(self, columnIndex):
'''
Used by the Java Swing UI
'''
cols = ["Time added", "Tool", "URL", "Issue", "Who"]
try:
return cols[columnIndex]
except KeyError:
return ""
def get(self, rowIndex):
'''
Gets the LogEntry at rowIndex
'''
return self._log.get(rowIndex)
def getValueAt(self, rowIndex, columnIndex):
'''
Used by the Java Swing UI
'''
logEntry = self._log.get(rowIndex)
if columnIndex == 0:
return logEntry.timestamp
elif columnIndex == 1:
return logEntry.tool.capitalize()
elif columnIndex == 2:
return logEntry.url
elif columnIndex == 3:
if logEntry.tool == "scanner":
return logEntry.issue_name
else:
return "N/A"
elif columnIndex == 4:
return logEntry.who
return ""
