def load_from_file(file_package,expected_class):
print("loading %s from %s" % (expected_class,file_package))
compiled_file = File(file_package.replace(".", "/") + "/" + expected_class + "$py.class")
source_file = File(file_package.replace(".", "/") + "/" + expected_class + ".py")
print("get request for controller %s. Compiled file outdated."%expected_class)
if compiled_file.exists():
if compiled_file.lastModified()<source_file.lastModified():
print("get request for controller %s. Compiled file outdated."%expected_class)
compiled_file.delete()
else:
print("get request for controller %s. Compiled file is up-to-date."%expected_class)
else:
print("get request for controller %s. Compiled file does not exists."%expected_class)
py_mod = imp.load_source("module_"+expected_class, source_file.getAbsolutePath())
if hasattr(py_mod, expected_class):
class_inst = getattr(py_mod,expected_class)
else:
class_inst =None
print(class_inst.__doc__)
print(class_inst.__name__)
return class_inst
def load_project(self, fname):
file = File(fname)
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
project = pm.loadProject(file)
print pm.status()
return project
def library_import(self, name, attributes):
# equals org.python.core.ClasspathPyImporter.PYCLASSPATH_PREFIX
if 'Jython' in platform.python_implementation():
import org.python.core.imp as jimp
if attributes['source']:
if '__pyclasspath__' in attributes['source']:
res = attributes['source'].split(
'__pyclasspath__')[1].replace(os.sep, '')
attributes['source'] = str(
jimp.getSyspathJavaLoader().getResources(
res).nextElement())
else:
try:
source_uri = jimp.getSyspathJavaLoader().getResources(
name + '.class').nextElement()
attributes['source'] = str(source_uri)
except:
pass
source_uri_txt = attributes['source']
if source_uri_txt and 'file:/' in source_uri_txt:
from java.io import File as File
from java.net import URL as URL
filePath = re.split('.*(?=file[:])', source_uri_txt)
if len(filePath) > 1:
path = re.split('[!][/]', filePath[1])[0]
f = File(URL(path).getFile())
source_uri_txt = f.getAbsolutePath()
attributes['source'] = source_uri_txt
self._send_to_server(AgentEventMessage.LIBRARY_IMPORT, name,
attributes)
def run_ant_target(build_file, target):
# Initializing DefaultLogger for all ant logs to go to console
ant_logger = DefaultLogger()
# Initializing Log4jListener to be able to log all ANT events to log file.
log_file = Log4jListener()
ant_logger.setErrorPrintStream(System.err)
ant_logger.setOutputPrintStream(System.out)
ant_logger.setMessageOutputLevel(Project.MSG_INFO)
build_fd = File(build_file)
project = Project()
if rb_config is not None:
enum = rb_config.keys()
while enum.hasMoreElements():
key = enum.nextElement()
project.setProperty(key, rb_config.getProperty(key))
project.setUserProperty('ant.file', build_fd.getAbsolutePath())
project.addBuildListener(ant_logger)
project.addBuildListener(log_file)
project.init()
helper = ProjectHelper.getProjectHelper()
project.addReference('ant.projectHelper', helper)
helper.parse(project, build_fd)
project.executeTarget(target)
def run_ant_target(build_file, target):
# Initializing DefaultLogger for all ant logs to go to console
ant_logger = DefaultLogger()
# Initializing Log4jListener to be able to log all ANT events to log file.
log_file = Log4jListener()
ant_logger.setErrorPrintStream(System.err)
ant_logger.setOutputPrintStream(System.out)
ant_logger.setMessageOutputLevel(Project.MSG_INFO)
build_fd = File(build_file)
project = Project()
if rb_config is not None:
enum = rb_config.keys()
while enum.hasMoreElements():
key = enum.nextElement()
project.setProperty(key, rb_config.getProperty(key))
project.setUserProperty('ant.file', build_fd.getAbsolutePath())
project.addBuildListener(ant_logger)
project.addBuildListener(log_file)
project.init()
helper = ProjectHelper.getProjectHelper()
project.addReference('ant.projectHelper', helper)
helper.parse(project, build_fd)
project.executeTarget(target)
def library_import(self, name, attributes):
# equals org.python.core.ClasspathPyImporter.PYCLASSPATH_PREFIX
import platform
if 'Jython' in platform.python_implementation():
import org.python.core.imp as jimp
if attributes['source']:
if '__pyclasspath__' in attributes['source']:
res = attributes['source'].split('__pyclasspath__')[1].replace(os.sep, '')
attributes['source'] = str(jimp.getSyspathJavaLoader().getResources(res).nextElement())
else:
try:
source_uri = jimp.getSyspathJavaLoader().getResources(name + '.class').nextElement()
attributes['source'] = str(source_uri)
except:
pass
source_uri_txt = attributes['source']
if source_uri_txt and 'file:/' in source_uri_txt:
import re
from java.io import File as File
from java.net import URL as URL
filePath = re.split('.*(?=file[:])', source_uri_txt)
if len(filePath) > 1:
path = re.split('[!][/]', filePath[1])[0]
f = File(URL(path).getFile())
source_uri_txt = f.getAbsolutePath()
attributes['source'] = source_uri_txt
self._send_socket("library_import", name, attributes)
def getRExecPathname(self):
if self.getArchitecture() != "x86_64":
raise Exception("Architecture not supported.")
plugin = PluginsLocator.getManager().getPlugin(
"org.gvsig.r.app.mainplugin")
pluginFolder = plugin.getPluginDirectory()
if self.getOperatingSystem() == "win":
f = File(pluginFolder, "R/bin/x64/Rterm.exe")
return f.getAbsolutePath().replace("\\", "/")
if self.getOperatingSystem() == "lin":
f = File(pluginFolder, "R/bin/R")
return f.getAbsolutePath()
raise Exception("Operating system not supported.")
def main():
if param_repository != None:
global uri, folder
uri = param_repository.get('uri') or DEFAULT_URI
name = param_repository.get('name') or DEFAULT_NAME
folder = File(NodelHost.instance().recipes().getRoot(), name)
console.info('Clone and pull folder: "%s"' % folder.getAbsolutePath())
def test_inputs(test_name):
spec_file = File(SPEC_DIR, test_name + ".spec")
inputs_file = File(INPUT_DIR, test_name + ".vm")
# If the inputs do not exist, generate them
# If the inputs are outdated, update them if the user wants to
if ((inputs_file.canRead() and UPDATE_INPUTS_ON_SPEC_CHANGE
and spec_file.canRead() and is_newer_than(spec_file, inputs_file))
or not inputs_file.canRead()):
cmd = TestGeneratorCommand()
cmd.parseArgs([
spec_file.getAbsolutePath(),
str(NUMBER_INPUTS_ON_SPEC_CHANGE), "--output",
inputs_file.getAbsolutePath()
])
cmd.run()
return build_velocity_context(inputs_file)
def updateSimsRunning():
for sim in allRunningSims:
timeFile = File(project.getProjectMainDirectory(), "simulations/"+sim+"/time.dat")
timeFile2 = File(project.getProjectMainDirectory(), "simulations/"+sim+"/time.txt") # for PSICS...
print "Checking file: "+timeFile.getAbsolutePath() +", exists: "+ str(timeFile.exists())
if (timeFile.exists()):
allFinishedSims.append(sim)
allRunningSims.remove(sim)
else:
print "Checking file: "+timeFile2.getAbsolutePath() +", exists: "+ str(timeFile2.exists())
if (timeFile2.exists()):
allFinishedSims.append(sim)
allRunningSims.remove(sim)
print "allFinishedSims: "+str(allFinishedSims)
print "allRunningSims: "+str(allRunningSims)
def lstat(path):
"""lstat(path) -> stat result
Like stat(path), but do not follow symbolic links.
"""
abs_path = sys.getPath(path)
try:
return stat_result.from_jnastat(_posix.lstat(abs_path))
except NotImplementedError:
pass
except:
raise
f = File(sys.getPath(path))
# XXX: jna-posix implements similar link detection in
# JavaFileStat.calculateSymlink, fallback to that instead when not
# native
abs_parent = f.getAbsoluteFile().getParentFile()
if not abs_parent:
# root isn't a link
return stat(path)
can_parent = abs_parent.getCanonicalFile()
if can_parent.getAbsolutePath() == abs_parent.getAbsolutePath():
# The parent directory's absolute path is canonical..
if f.getAbsolutePath() != f.getCanonicalPath():
# but the file's absolute and canonical paths differ (a
# link)
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# The parent directory's path is not canonical (one of the parent
# directories is a symlink). Build a new path with the parent's
# canonical path and compare the files
f = File(_path.join(can_parent.getAbsolutePath(), f.getName()))
if f.getAbsolutePath() != f.getCanonicalPath():
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# Not a link, only now can we determine if it exists (because
# File.exists() returns False for dead links)
if not f.exists():
raise OSError(errno.ENOENT, strerror(errno.ENOENT), path)
return stat(path)
def lstat(path):
"""lstat(path) -> stat result
Like stat(path), but do not follow symbolic links.
"""
abs_path = sys.getPath(path)
try:
return stat_result.from_jnastat(_posix.lstat(abs_path))
except NotImplementedError:
pass
except:
raise
f = File(sys.getPath(path))
# XXX: jna-posix implements similar link detection in
# JavaFileStat.calculateSymlink, fallback to that instead when not
# native
abs_parent = f.getAbsoluteFile().getParentFile()
if not abs_parent:
# root isn't a link
return stat(path)
can_parent = abs_parent.getCanonicalFile()
if can_parent.getAbsolutePath() == abs_parent.getAbsolutePath():
# The parent directory's absolute path is canonical..
if f.getAbsolutePath() != f.getCanonicalPath():
# but the file's absolute and canonical paths differ (a
# link)
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# The parent directory's path is not canonical (one of the parent
# directories is a symlink). Build a new path with the parent's
# canonical path and compare the files
f = File(_path.join(can_parent.getAbsolutePath(), f.getName()))
if f.getAbsolutePath() != f.getCanonicalPath():
return stat_result((_stat.S_IFLNK, 0, 0, 0, 0, 0, 0, 0, 0, 0))
# Not a link, only now can we determine if it exists (because
# File.exists() returns False for dead links)
if not f.exists():
raise OSError(errno.ENOENT, strerror(errno.ENOENT), path)
return stat(path)
def saved(controller, newValue):
global __UI__
if pause.value:
return
newCount = int(newValue.getStringData())
axis_name.value = scan_variable_node.getValue().getStringData()
# __UI__.getScriptExecutor().runScript(cmd)
log('scanpoint=' + str(scanpoint_node.getValue().getIntData() + 1), __writer__)
if newCount > 0:
try:
checkFile = File(filenameNode.getValue().getStringData())
dataPath = System.getProperty('sics.data.path')
checkFile = File(dataPath + "/" + checkFile.getName())
filePath = checkFile.getAbsolutePath()
if not checkFile.exists():
log("The target file :" + checkFile.getAbsolutePath() + " can not be found")
dataSourceViewer.addDataset(filePath, True)
except:
log('failed to load the file')
def EzFileDialog(initialFile, save, stage=None):
from javafx.stage import FileChooser
from java.io import File
dlg = FileChooser()
if initialFile:
f = File(initialFile)
if f.exists():
if f.isDirectory(): dlg.setInitialDirectory(f)
if f.isFile(): dlg.setInitialFileName(f.getAbsolutePath());
dlg.setTitle("Select File");
if save: return dlg.showSaveDialog(stage);
else: return dlg.showOpenDialog(stage);
def load_session(req,session_dir):
if req.params.has_key("mvcx.sessionID"):
session_file=File("%s/%s.json" % (session_dir,req.params["mvcx.sessionID"]))
print("session_path:"+str(session_file.getAbsolutePath()))
if session_file.exists():
session=JsonObject("\n".join(Files.readLines(session_file,Charset.defaultCharset())))
return session
else:
return None
else:
return None
def updated(controller, newValue):
global Plot1
global data
global axis
global fileId
print 'updated'
newCount = int(newValue.getStringData())
scanpoint = scanpoint_node.getValue().getIntData()
variable_value = scan_variable_value_node.getValue().getFloatData()
if scanpoint == 1:
data = [newCount]
axis = [variable_value]
else:
data.append(newCount)
axis.append(variable_value)
variable_name = scan_variable_node.getValue().getStringData()
axis_name.value = variable_name
try:
checkFile = File(filenameNode.getValue().getStringData())
dataPath = System.getProperty('sics.data.path')
checkFile = File(dataPath + "/" + checkFile.getName())
filePath = checkFile.getAbsolutePath()
if not checkFile.exists():
print "The target file :" + checkFile.getAbsolutePath() + " can not be found";
dataSourceViewer.addDataset(filePath, False)
fileId = checkFile.getName()
if fileId.__contains__('TPN') and fileId.__contains__('.nx.hdf'):
fileId = str(int(fileId[3 : 10]))
except:
print 'failed to load the file'
fileId = variable_name
print fileId
ds = Dataset(data, axes = [axis], title = fileId)
print ds
Plot1.set_dataset(ds)
Plot1.x_label = variable_name
Plot1.y_label = 'counts'
Plot1.title = 'counts vs ' + variable_name
def __get_manifest(self, source_path, from_archive):
"""
Returns the manifest object for the specified path.
The source path may be a jar, or an exploded path.
:param source_path: the source path to be checked
:param from_archive: if True, use the manifest from the archive, otherwise from the file system
:return: the manifest, or None if it is not present
:raises: IOException: if there are problems reading an existing manifest
"""
manifest = None
if string_utils.is_empty(source_path):
return manifest
source_path = self.model_context.replace_token_string(source_path)
if from_archive and deployer_utils.is_path_into_archive(source_path):
return self.archive_helper.get_manifest(source_path)
else:
if not os.path.isabs(source_path):
# if this was in archive, it has been expanded under domain home.
# or it may be a relative file intentionally placed under domain home.
source_file = File(File(self.model_context.get_domain_home()), source_path)
else:
source_file = File(source_path)
if source_file.isDirectory():
# read the manifest directly from the file system
manifest_file = File(source_file, MANIFEST_NAME)
if manifest_file.exists():
stream = None
try:
stream = FileInputStream(manifest_file)
manifest = Manifest(stream)
finally:
if stream is not None:
try:
stream.close()
except IOException:
# nothing to report
pass
else:
# read the manifest from the deployable ear/jar/war on the file system
archive = JarFile(source_file.getAbsolutePath())
manifest = archive.getManifest()
return manifest
def valueChanged(self, controller, newValue):
global __file_to_add__
newCount = int(newValue.getStringData())
if newCount != self.saveCount:
self.saveCount = newCount
try:
checkFile = File(__file_name_node__.getValue().getStringData())
checkFile = File(__data_folder__ + "/" + checkFile.getName())
__file_to_add__ = checkFile.getAbsolutePath()
if not checkFile.exists():
print "The target file :" + __file_to_add__ + " can not be found"
return
runnable = __Display_Runnable__()
runnable.run = add_dataset
Display.getDefault().asyncExec(runnable)
except:
print 'failed to add dataset ' + __file_to_add__
def save_session(req,remember,session_dir,**kwargs):
session=JsonObject()
id=str(uuid.uuid1())
session.putString("id", id)
for name,value in kwargs.iteritems():
session.putString(name, value)
print("remember = "+remember)
cookie = 'mvcx.sessionID=%s' % id.strip()
if remember=="1":
cookie += ";max-age=864000"
req.response.put_header('set-cookie', cookie)
session_file=File("%s/%s.json" % (session_dir,id))
print("session_path:"+str(session_file.getAbsolutePath()))
session_file.getParentFile().mkdirs()
Files.write(str(session),session_file)
def valueChanged(self, controller, newValue):
global __file_to_add__
newCount = int(newValue.getStringData());
if newCount != self.saveCount:
self.saveCount = newCount;
try:
checkFile = File(__file_name_node__.getValue().getStringData());
checkFile = File(__data_folder__ + "/" + checkFile.getName());
__file_to_add__ = checkFile.getAbsolutePath();
if not checkFile.exists():
print "The target file :" + __file_to_add__ + " can not be found";
return
runnable = __Display_Runnable__()
runnable.run = add_dataset
Display.getDefault().asyncExec(runnable)
except:
print 'failed to add dataset ' + __file_to_add__
def find_command_build_file(build_dir, target):
for build_name in os.listdir(build_dir):
if is_xml(build_name):
build_file = os.path.join(build_dir, build_name)
if os.path.isfile(build_file):
try:
build_fd = File(build_file)
project = Project()
project.setUserProperty('ant.file', build_fd.getAbsolutePath())
project.init()
helper = ProjectHelper.getProjectHelper()
project.addReference('ant.projectHelper', helper)
project.setProperty('ConfigNOW.home', os.getcwd())
helper.parse(project, build_fd)
if project.getTargets().containsKey(target):
return build_file
except:
log.error('Ant build file ' + str(build_file) + ' could not be processed')
print sys.exc_info()
def find_command_build_file(build_dir, target):
for build_name in os.listdir(build_dir):
if is_xml(build_name):
build_file = os.path.join(build_dir, build_name)
if os.path.isfile(build_file):
try:
build_fd = File(build_file)
project = Project()
project.setUserProperty('ant.file',
build_fd.getAbsolutePath())
project.init()
helper = ProjectHelper.getProjectHelper()
project.addReference('ant.projectHelper', helper)
project.setProperty('ConfigNOW.home', os.getcwd())
helper.parse(project, build_fd)
if project.getTargets().containsKey(target):
return build_file
except:
log.error('Ant build file ' + str(build_file) +
' could not be processed')
print sys.exc_info()
def updateCmdForDeltaScanning(commandLine, Framework):
originalScanFileFolderPath = CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.ORIGINAL_FOLDER_NAME
originalScanFile = File(originalScanFileFolderPath,
InventoryUtils.generateScanFileName(Framework))
if originalScanFile.exists():
scan = None
try:
try:
buffer = jarray.zeros(0x24, 'b')
fileSize = originalScanFile.length()
if fileSize > 0x24:
scan = RandomAccessFile(originalScanFile, "r")
scan.readFully(buffer)
if (buffer[0] == 0x1F) and (
(buffer[1] & 0xFF) == 0x8B) and (buffer[2] == 0x08):
scan.seek(fileSize - 8)
scan.readFully(buffer, 0, 8)
crc32 = getInt(buffer, 0)
size = getInt(buffer, 4)
deltaParams = ' -oldscanid:' + str(
crc32) + ' -oldscansize:' + str(size) + ' '
index = String(commandLine).indexOf(
ENTERPRISE_MODE) + String(
ENTERPRISE_MODE).length()
commandLine = commandLine[
0:index] + deltaParams + commandLine[index + 1:]
logger.debug('Scanner execution command updated to ',
commandLine)
except:
logger.debugException(
"Failed to calculate CRC32 and size of zipped scan file " +
originalScanFile.getAbsolutePath())
finally:
if scan is not None:
try:
scan.close()
except:
pass
return commandLine
def testAll(argv=None):
if argv is None:
argv = sys.argv
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath() + ", exists: " + str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
defSimConfig = project.simConfigInfo.getDefaultSimConfig()
cellsOnlySimConfig = project.simConfigInfo.getSimConfig("CellsOnly")
pharyngealSimConfig = project.simConfigInfo.getSimConfig("PharyngealNeurons")
expectedNumberCells = 302
##########################
print "\n----- Test 1: Check number of cells in sim config " + defSimConfig.getName() + "..."
pm.doGenerate(defSimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(defSimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
print "\n---- Test 2: number of cells in sim config " + cellsOnlySimConfig.getName() + "..."
pm.doGenerate(cellsOnlySimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(cellsOnlySimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
filename = "../../CElegansNeuronTables.xls"
print "\n---- Test 3: confirm settings in project match those in " + filename + "..."
from xlrd import open_workbook
rb = open_workbook(filename)
print "Opened Excel file: " + filename
confirmed = 0
prefix = "NCXLS_"
for row in range(1, rb.sheet_by_index(0).nrows):
pre = rb.sheet_by_index(0).cell(row, 0).value
post = rb.sheet_by_index(0).cell(row, 1).value
syntype = rb.sheet_by_index(0).cell(row, 2).value
num = int(rb.sheet_by_index(0).cell(row, 3).value)
synclass = rb.sheet_by_index(0).cell(row, 4).value
# print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
netConnName = prefix + pre + "_" + post
if "GapJunction" in syntype:
netConnName = netConnName + "_GJ"
src = project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName)
tgt = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
if not (src == pre and tgt == post):
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" % (
row,
num,
pre,
post,
syntype,
synclass,
)
print "*** Couldn't find connection: %s, src: %s, tgt: %s" % (netConnName, src, tgt)
assert src == pre
assert tgt == post
if src == tgt:
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" % (
row,
num,
pre,
post,
syntype,
synclass,
)
print "*** This connection is from: %s, src: %s, tgt: %s, synaptic connection on same cell!!" % (
netConnName,
src,
tgt,
)
confirmed += 1
print "Confirmed %i connections in project match spreadsheet" % confirmed
havePrefix = 0
allNetConnNames = project.morphNetworkConnectionsInfo.getAllSimpleNetConnNames()
for name in allNetConnNames:
if name.startswith(prefix):
havePrefix += 1
print "Project contains %i Network connections starting with %s" % (havePrefix, prefix)
assert havePrefix == confirmed
##########################
print "\n---- Test 4: number of cells in sim config " + pharyngealSimConfig.getName() + "..."
pm.doGenerate(pharyngealSimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: " + str(pharyngealSimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i" % (numCells, numConns)
expectedCells = 20
expectedNetConns = 269
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
print "\n------------------------------------------All tests completed!\n"
exit()
try:
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from math import *
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
# Add a number of cells to the generatedCellPositions, connections to generatedNetworkConnections
# and electrical inputs to generatedElecInputs
numCells = 12
for i in range(0, numCells):
x = 100 * sin(i * 2 * pi / numCells)
y = 100 * cos(i * 2 * pi / numCells)
myProject.generatedCellPositions.addPosition("SampleCellGroup", i, x, y, 0)
if i != numCells - 1:
def updateCmdForDeltaScanning(commandLine, Framework):
originalScanFileFolderPath = CollectorsParameters.PROBE_MGR_INVENTORY_XMLENRICHER_FILES_FOLDER + XmlEnricherConstants.ORIGINAL_FOLDER_NAME
originalScanFile = File(originalScanFileFolderPath, InventoryUtils.generateScanFileName(Framework))
if originalScanFile.exists():
scan = None
try:
try:
buffer = jarray.zeros(0x24, 'b')
fileSize = originalScanFile.length()
if fileSize > 0x24:
scan = RandomAccessFile(originalScanFile, "r")
scan.readFully(buffer)
if (buffer[0] == 0x1F) and ((buffer[1] & 0xFF) == 0x8B) and (buffer[2] == 0x08):
scan.seek(fileSize - 8)
scan.readFully(buffer, 0, 8)
crc32 = getInt(buffer, 0)
size = getInt(buffer, 4)
deltaParams = ' -oldscanid:' + str(crc32) + ' -oldscansize:' + str(size) + ' '
index = String(commandLine).indexOf(ENTERPRISE_MODE) + String(ENTERPRISE_MODE).length()
commandLine = commandLine[0:index] + deltaParams + commandLine[index + 1:]
logger.debug('Scanner execution command updated to ', commandLine)
except:
logger.debugException("Failed to calculate CRC32 and size of zipped scan file " + originalScanFile.getAbsolutePath())
finally:
if scan is not None:
try:
scan.close()
except:
pass
return commandLine
try:
dh = JFileUtils.validateExistingDirectory(value)
except JIllegalArgumentException, iae:
ex = exception_helper.create_cla_exception(
'WLSDPLY-01606', value, iae.getLocalizedMessage(), error=iae)
ex.setExitCode(self.ARG_VALIDATION_ERROR_EXIT_CODE)
self._logger.throwing(ex,
class_name=self._class_name,
method_name=method_name)
raise ex
config_xml = JFile(dh, 'config/config.xml')
try:
config_xml = JFileUtils.validateExistingFile(
config_xml.getAbsolutePath())
except JIllegalArgumentException, iae:
ex = exception_helper.create_cla_exception(
'WLSDPLY-01607',
dh.getAbsolutePath(),
config_xml.getAbsolutePath(),
iae.getLocalizedMessage(),
error=iae)
ex.setExitCode(self.ARG_VALIDATION_ERROR_EXIT_CODE)
self._logger.throwing(ex,
class_name=self._class_name,
method_name=method_name)
raise ex
return dh.getAbsolutePath()
import com.hanhuy.keepassj.PwDatabase as PwDatabase
import com.hanhuy.keepassj.KdbxFormat as KdbxFormat
import com.hanhuy.keepassj.CompositeKey as CompositeKey
import com.hanhuy.keepassj.KcpPassword as KcpPassword
import com.hanhuy.keepassj.IOConnectionInfo as IOConnectionInfo
import java.io.File as File
# Main
print "Here"
dbFile = File("/tmp/test.kdbx")
db = PwDatabase()
key = CompositeKey()
key.AddUserKey(KcpPassword("1234"))
db.Open(IOConnectionInfo.FromPath(dbFile.getAbsolutePath()), key, None)
print str(db.getKeyEncryptionRounds())
i = db.getRootGroup().GetEntries(True).GetAt(0).getStrings().iterator()
while i.hasNext():
print i.next()
print ""
ps = db.getRootGroup().GetEntries(True).GetAt(0).getStrings().Get("Password")
print ps
print ps.ReadString()
db.Close()
print "Done"
def create_setenv(home_dir):
main_logger.info('Creating setenv file')
str_home_dir=str(home_dir)
wls_name=rb_config.getProperty('wls.name')
weblogic_loc=os.path.join(str_home_dir, wls_name)
weblogic_jar_loc=os.path.join(weblogic_loc,'server/lib/weblogic.jar')
weblogic_cp_jar_loc=os.path.join(str_home_dir, wls_name,'modules/features/wlst.wls.classpath.jar')
weblogic_jar=File(weblogic_jar_loc)
weblogic_cp_jar=File(weblogic_cp_jar_loc)
separator = os.sep
classpathSep=os.pathsep
osb_name=rb_config.getProperty('osb.name')
osb_jar=""
osb_api_jar=""
osb_wls_jar=""
util_jar = os.getcwd() + '/core/engine/lib/ConfigNOWUtils.jar'
if(home_dir and osb_name):
osb_jar=os.path.join(home_dir,osb_name,'lib/osb-server-modules-ref.jar')
osb_api_jar=os.path.join(home_dir,osb_name,'lib/sb-kernel-api.jar')
osb_wls_jar=os.path.join(home_dir,osb_name,'lib/sb-kernel-wls.jar')
main_logger.debug(osb_jar)
if separator is not None and classpathSep is not None:
pathSep=os.sep
if classpathSep==';':
main_logger.info('Assumed windows operating system')
envfile='setenv.cmd'
envcommand='set CLASSPATH=' + str(weblogic_cp_jar) + classpathSep + str(weblogic_jar) + classpathSep + util_jar
if (osb_jar is not None and len(osb_jar) > 0):
envcommand += classpathSep + str(osb_jar)
envcommand += classpathSep + str(osb_api_jar)
envcommand += classpathSep + str(osb_wls_jar)
envcommand +='\nset COMMON_COMPONENTS_HOME='+ str_home_dir + '/oracle_common'
setWLSEnv=File(weblogic_loc, '/server/bin/setWLSEnv.cmd')
else:
main_logger.info('Assumed linux operating system')
envfile='setenv.sh'
envcommand='CLASSPATH=' + str(weblogic_cp_jar) + classpathSep + str(weblogic_jar) + classpathSep + util_jar
setWLSEnv=File(weblogic_loc, '/server/bin/setWLSEnv.sh')
if (osb_jar is not None and len(osb_jar) > 0):
envcommand += classpathSep + str(osb_jar)
if weblogic_loc is not None:
print 'weblogic_loc = ' +str(weblogic_loc)
else:
print 'weblogic_loc is null'
print 'Command = ' + envcommand
print 'setWLSEnv = ' +str(setWLSEnv)
envcommand=envcommand + '\n. ' + str(setWLSEnv) + ' > /dev/null'
envcommand=envcommand +'\nexport COMMON_COMPONENTS_HOME='+ str_home_dir + '/oracle_common'
if weblogic_jar.exists():
if os.path.isfile(envfile):
os.remove(envfile)
setenv=open(envfile,'w')
setenv.write(envcommand)
setenv.close()
main_logger.info('Located weblogic.jar at ' + str(weblogic_jar))
return True
else:
main_logger.debug('Could not find JAR file ' + weblogic_jar.getAbsolutePath()+'Please check wls.oracle.home and wls.name properties')
if os.path.exists(envfile):
os.remove(envfile)
envcommand='set CLASSPATH=' + util_jar
setenv=open(envfile,'w')
setenv.write(envcommand)
setenv.close()
return True
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
from ucl.physiol.neuroconstruct.simulation import SimulationData
from ucl.physiol.neuroconstruct.simulation import SpikeAnalyser
from math import *
import time
neuroConstructSeed = 1234
simulatorSeed = 4321
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
simConfig = myProject.simConfigInfo.getSimConfig("SingleCell")
pm.doGenerate(simConfig.getName(), neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated..."
time.sleep(2)
numGenerated = myProject.generatedCellPositions.getNumberInAllCellGroups()
def jython_start(ctx):
from net.sf.chellow.billing import Contract
from net.sf.chellow.monad import Hiber
from org.python.util import PythonInterpreter
from java.io import LineNumberReader, File, FileReader
from org.python.core import PyString
interp = PythonInterpreter()
sys_state = interp.getSystemState()
lib_path = ctx.getRealPath("/WEB-INF/lib-python")
if lib_path is not None:
lib_dir = File(lib_path)
if lib_dir.exists():
sys_state.path.append(PyString(lib_path))
# Now check for .pth files in lib-python and process each one
for lib_content in lib_dir.list():
if lib_content.endswith(".pth"):
line_reader = None
try:
line_reader = LineNumberReader(
FileReader(File(lib_path, lib_content)))
line = line_reader.readLine()
while line is not None:
line = line.strip()
if len(line) == 0:
continue
if line.startswith("#"):
continue
if line.startswith("import"):
efunc = getattr(interp, 'exec')
efunc(line)
continue
archive_file = File(lib_path, line)
archive_real_path = archive_file.getAbsolutePath()
sys_state.path.append(PyString(archive_real_path))
line = line_reader.readLine()
finally:
line_reader.close()
for contract_name in LIBS:
contract = Contract.getNonCoreContract(contract_name)
nspace = LibDict()
nspace['db_id'] = contract.id
exec(contract.getChargeScript(), nspace)
for k, v in nspace.iteritems():
if not hasattr(nspace, k):
setattr(nspace, k, v)
ctx.setAttribute("net.sf.chellow." + contract_name, nspace)
Hiber.close()
logger.log(str(id) + ' - ' + str(model.getTrackModel().trackEdges(id))) #---------------- # Display results #---------------- sb = SAXBuilder() document = sb.build( file ) root = document.getRootElement() settingsElement = root.getChild( SETTINGS_ELEMENT_KEY ) imageInfoElement = settingsElement.getChild( IMAGE_ELEMENT_KEY ); filename = imageInfoElement.getAttributeValue( IMAGE_FILENAME_ATTRIBUTE_NAME ); folder = imageInfoElement.getAttributeValue( IMAGE_FOLDER_ATTRIBUTE_NAME ); imageFile = File( folder, filename ); dsel = root.getChild(DISPLAY_SETTINGS_ELEMENT_KEY); imp = IJ.openImage( imageFile.getAbsolutePath() ); #--------------------------------------- # Building a settings object from a file #--------------------------------------- # Reading the Settings object is actually currently complicated. The # reader wants to initialize properly everything you saved in the file, # including the spot, edge, track analyzers, the filters, the detector, # the tracker, etc... # It can do that, but you must provide the reader with providers, that # are able to instantiate the correct TrackMate Java classes from # the XML data. # We start by creating an empty settings object
# set the parameters
newAccountSet = False
contextAccount = moneydance_ui.firstMainFrame.getSelectedAccount()
filename = fileToImport.getName()
extension = os.path.splitext(filename)[1].upper()
if moneydance_data is None: raise Exception("ERROR - No data")
wrapper = moneydance_ui.getCurrentAccounts() # type: AccountBookWrapper
book = moneydance_data
importWasSuccessful = True
dirName = fileToImport.getParent()
try:
fPath = fileToImport.getAbsolutePath() # type: str
fPath = fPath.upper().strip()
if not moneydance_ui.saveCurrentAccount():
raise Exception("ERROR Save Failed")
importer = moneydance_ui.getFileImporter(
fileToImport) # type: FileImporter
if (importer is not None):
if i_want_popups:
import_option = JOptionPane.showInputDialog(
None, "Select Import Type", "IMPORT",
JOptionPane.INFORMATION_MESSAGE,
moneydance_ui.getIcon(
"/com/moneydance/apps/md/view/gui/glyphs/appicon_64.png"),
ImportDataSourceType.values(),
importer.getSpec().getSourceType())
elif line.startswith('login '):
user = line[6:]
elif line.startswith('password '):
password = line[9:]
elif line.startswith('machine '):
break
f.close()
from java.io import File
jssecacerts = File('jssecacerts')
if jssecacerts.exists():
from java.lang import System
System.setProperty('javax.net.ssl.trustStore',
jssecacerts.getAbsolutePath())
from fiji import MediaWikiClient
client = MediaWikiClient(url)
if user != None and password != None and not client.isLoggedIn():
client.logIn(user, password)
response = client.sendRequest(
['title', 'Special:RecentChanges', 'hidebots', '0'], None)
if client.isLoggedIn():
client.logOut()
def parse_time(string):
m = search('\\d\\d:\\d\\d', string)
if m is None:
#
try:
from java.io import File
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
morphDir = File(
"../osb/showcase/neuroConstructShowcase/Ex3_Morphology/importedMorphologies/"
)
morphmlFile = File(morphDir, "SimplePurkinjeCell.morph.xml")
print "Going to load morphology from: " + morphmlFile.getCanonicalPath()
converter = MorphMLConverter()
cell = converter.loadFromMorphologyFile(morphmlFile, "NewCell")
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
from math import *
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath() + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
# Add a number of cells to the generatedCellPositions, connections to generatedNetworkConnections
# and electrical inputs to generatedElecInputs
numCells = 12
for i in range(0, numCells):
x = 100 * sin(i * 2 * pi / numCells)
y = 100 * cos(i * 2 * pi / numCells)
myProject.generatedCellPositions.addPosition("SampleCellGroup", i, x, y, 0)
def create_setenv(home_dir):
main_logger.info('Creating setenv file')
str_home_dir = str(home_dir)
wls_name = rb_config.getProperty('wls.name')
weblogic_loc = os.path.join(str_home_dir, wls_name)
weblogic_jar_loc = os.path.join(weblogic_loc, 'server/lib/weblogic.jar')
weblogic_cp_jar_loc = os.path.join(
str_home_dir, wls_name, 'modules/features/wlst.wls.classpath.jar')
weblogic_jar = File(weblogic_jar_loc)
weblogic_cp_jar = File(weblogic_cp_jar_loc)
separator = os.sep
classpathSep = os.pathsep
util_jar = os.getcwd() + '/core/engine/lib/wlsPaasUtils.jar'
if separator is not None and classpathSep is not None:
pathSep = os.sep
if classpathSep == ';':
main_logger.info('Assumed windows operating system')
envfile = 'setenv.cmd'
envcommand = 'set CLASSPATH=' + str(
weblogic_cp_jar) + classpathSep + str(
weblogic_jar) + classpathSep + util_jar
wlstargs = '\nset ARGS=-Dweblogic.security.SSL.enableJSSE=true -Dweblogic.security.SSL.ignoreHostnameVerification=true -Dweblogic.security.TrustKeyStore=DemoTrust -Djava.security.egd=file:/dev/./urandom -Dweblogic.security.SSL.protocolVersion=TLS1'
else:
main_logger.info('Assumed linux operating system')
envfile = 'setenv.sh'
envcommand = 'CLASSPATH=' + str(
weblogic_cp_jar) + classpathSep + str(
weblogic_jar) + classpathSep + util_jar
wlstargs = '\nARGS="-Dweblogic.security.SSL.enableJSSE=true -Dweblogic.security.SSL.ignoreHostnameVerification=true -Dweblogic.security.TrustKeyStore=DemoTrust -Djava.security.egd=file:/dev/./urandom -Dweblogic.security.SSL.protocolVersion=TLS1"'
setWLSEnv = File(weblogic_loc, '/server/bin/setWLSEnv.sh')
if weblogic_loc is not None:
print 'weblogic_loc = ' + str(weblogic_loc)
else:
print 'weblogic_loc is null'
print 'Command = ' + envcommand
print 'setWLSEnv = ' + str(setWLSEnv)
envcommand = envcommand + '\n. ' + str(setWLSEnv) + ' > /dev/null'
envcommand = envcommand + '\nexport COMMON_COMPONENTS_HOME=' + str_home_dir + '/oracle_common'
if weblogic_jar.exists():
if os.path.isfile(envfile):
os.remove(envfile)
setenv = open(envfile, 'w')
setenv.write(envcommand)
setenv.write(wlstargs)
setenv.close()
main_logger.info('Located weblogic.jar at ' + str(weblogic_jar))
return True
else:
main_logger.debug(
'Could not find JAR file ' + weblogic_jar.getAbsolutePath() +
'Please check wls.oracle.home and wls.name properties')
if os.path.exists(envfile):
os.remove(envfile)
envcommand = 'set CLASSPATH=' + util_jar
setenv = open(envfile, 'w')
setenv.write(envcommand)
setenv.write(wlstargs)
setenv.close()
return True
import os
try:
from java.io import File
except ImportError:
print "Note: this file should be run using ..\\..\\..\\nC.bat -python XXX.py' or '../../../nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
sys.path.append(os.environ["NC_HOME"]+"/pythonNeuroML/nCUtils")
import ncutils as nc
projFile = File(os.getcwd(), "../Ex4_HHcell.ncx")
print "Project file for this test: "+ projFile.getAbsolutePath()
############## Main settings ##################
simConfigs = []
simConfigs.append("Default Simulation Configuration")
simDt = 0.001
simulators = ["NEURON", "GENESIS_PHYS", "GENESIS_SI", "MOOSE_PHYS", "MOOSE_SI"]
simulators = ["NEURON", "GENESIS_PHYS", "GENESIS_SI"]
# simulators = ["NEURON", "LEMS"]
def create_setenv(home_dir):
main_logger.info('Creating setenv file')
str_home_dir = str(home_dir)
wls_name = rb_config.getProperty('wls.name')
weblogic_loc = os.path.join(str_home_dir, wls_name)
weblogic_jar_loc = os.path.join(weblogic_loc, 'server/lib/weblogic.jar')
weblogic_cp_jar_loc = os.path.join(
str_home_dir, wls_name, 'modules/features/wlst.wls.classpath.jar')
weblogic_jar = File(weblogic_jar_loc)
weblogic_cp_jar = File(weblogic_cp_jar_loc)
separator = os.sep
classpathSep = os.pathsep
osb_name = rb_config.getProperty('osb.name')
osb_jar = ""
osb_api_jar = ""
osb_wls_jar = ""
util_jar = os.getcwd() + '/core/engine/lib/ConfigNOWUtils.jar'
if (home_dir and osb_name):
osb_jar = os.path.join(home_dir, osb_name,
'lib/osb-server-modules-ref.jar')
osb_api_jar = os.path.join(home_dir, osb_name, 'lib/sb-kernel-api.jar')
osb_wls_jar = os.path.join(home_dir, osb_name, 'lib/sb-kernel-wls.jar')
main_logger.debug(osb_jar)
if separator is not None and classpathSep is not None:
pathSep = os.sep
if classpathSep == ';':
main_logger.info('Assumed windows operating system')
envfile = 'setenv.cmd'
envcommand = 'set CLASSPATH=' + str(
weblogic_cp_jar) + classpathSep + str(
weblogic_jar) + classpathSep + util_jar
if (osb_jar is not None and len(osb_jar) > 0):
envcommand += classpathSep + str(osb_jar)
envcommand += classpathSep + str(osb_api_jar)
envcommand += classpathSep + str(osb_wls_jar)
envcommand += '\nset COMMON_COMPONENTS_HOME=' + str_home_dir + '/oracle_common'
setWLSEnv = File(weblogic_loc, '/server/bin/setWLSEnv.cmd')
else:
main_logger.info('Assumed linux operating system')
envfile = 'setenv.sh'
envcommand = 'CLASSPATH=' + str(
weblogic_cp_jar) + classpathSep + str(
weblogic_jar) + classpathSep + util_jar
setWLSEnv = File(weblogic_loc, '/server/bin/setWLSEnv.sh')
if (osb_jar is not None and len(osb_jar) > 0):
envcommand += classpathSep + str(osb_jar)
if weblogic_loc is not None:
print 'weblogic_loc = ' + str(weblogic_loc)
else:
print 'weblogic_loc is null'
print 'Command = ' + envcommand
print 'setWLSEnv = ' + str(setWLSEnv)
envcommand = envcommand + '\n. ' + str(setWLSEnv) + ' > /dev/null'
envcommand = envcommand + '\nexport COMMON_COMPONENTS_HOME=' + str_home_dir + '/oracle_common'
if weblogic_jar.exists():
if os.path.isfile(envfile):
os.remove(envfile)
setenv = open(envfile, 'w')
setenv.write(envcommand)
setenv.close()
main_logger.info('Located weblogic.jar at ' + str(weblogic_jar))
return True
else:
main_logger.debug(
'Could not find JAR file ' + weblogic_jar.getAbsolutePath() +
'Please check wls.oracle.home and wls.name properties')
if os.path.exists(envfile):
os.remove(envfile)
envcommand = 'set CLASSPATH=' + util_jar
setenv = open(envfile, 'w')
setenv.write(envcommand)
setenv.close()
return True
from ucl.physiol.neuroconstruct.project import ProjectManager
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
from ucl.physiol.neuroconstruct.cell.compartmentalisation import OriginalCompartmentalisation
from ucl.physiol.neuroconstruct.neuroml.NeuroMLConstants import NeuroMLLevel, NeuroMLVersion
if len(sys.argv) != 3:
print "Usage: \n ../nC.sh -python Ex7_ExtractNeuroML.py neuroConstruct_project_file folder_for_NeuroML"
print "Example: \n ../nC.sh -python Ex7_ExtractNeuroML.py TestPython/TestPython.neuro.xml /tmp"
print "or: \n ..\\nC.bat -python Ex7_ExtractNeuroML.py TestPython\\TestPython.neuro.xml c:\\temp"
sys.exit(1)
# Load neuroConstruct project
projFile = File(sys.argv[1])
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
saveDir = File(sys.argv[2])
print "Going to save NeuroML files to: " + saveDir.getAbsolutePath()
level = NeuroMLLevel.NEUROML_LEVEL_3
version = NeuroMLVersion.NEUROML_VERSION_1
MorphMLConverter.saveAllCellsInNeuroML(myProject,
OriginalCompartmentalisation(), level,
version, None, saveDir)
# The create domain operation should use the domain parent arg.
#
def _validate_domain_home_arg(self, value):
method_name = '_validate_domain_home_arg'
try:
dh = JFileUtils.validateExistingDirectory(value)
except JIllegalArgumentException, iae:
ex = exception_helper.create_cla_exception('WLSDPLY-01606', value, iae.getLocalizedMessage(), error=iae)
ex.setExitCode(self.ARG_VALIDATION_ERROR_EXIT_CODE)
self._logger.throwing(ex, class_name=self._class_name, method_name=method_name)
raise ex
config_xml = JFile(dh, 'config/config.xml')
try:
config_xml = JFileUtils.validateExistingFile(config_xml.getAbsolutePath())
except JIllegalArgumentException, iae:
ex = exception_helper.create_cla_exception('WLSDPLY-01607', dh.getAbsolutePath(),
config_xml.getAbsolutePath(),
iae.getLocalizedMessage(), error=iae)
ex.setExitCode(self.ARG_VALIDATION_ERROR_EXIT_CODE)
self._logger.throwing(ex, class_name=self._class_name, method_name=method_name)
raise ex
return dh.getAbsolutePath()
def get_domain_parent_key(self):
return self.DOMAIN_PARENT_SWITCH
def is_domain_parent_key(self, key):
return self.DOMAIN_PARENT_SWITCH == key
from ucl.physiol.neuroconstruct.cell.converters import MorphMLConverter
from ucl.physiol.neuroconstruct.cell.compartmentalisation import OriginalCompartmentalisation
from ucl.physiol.neuroconstruct.neuroml.NeuroMLConstants import NeuroMLLevel, NeuroMLVersion
if len(sys.argv) != 3:
print "Usage: \n ../nC.sh -python Ex7_ExtractNeuroML.py neuroConstruct_project_file folder_for_NeuroML"
print "Example: \n ../nC.sh -python Ex7_ExtractNeuroML.py TestPython/TestPython.neuro.xml /tmp"
print "or: \n ..\\nC.bat -python Ex7_ExtractNeuroML.py TestPython\\TestPython.neuro.xml c:\\temp"
sys.exit(1)
# Load neuroConstruct project
projFile = File(sys.argv[1])
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
print "Loaded project: " + myProject.getProjectName()
saveDir = File(sys.argv[2])
print "Going to save NeuroML files to: " + saveDir.getAbsolutePath()
level = NeuroMLLevel.NEUROML_LEVEL_3
version = NeuroMLVersion.NEUROML_VERSION_1
MorphMLConverter.saveAllCellsInNeuroML(myProject,
OriginalCompartmentalisation(),
level,
version,
def testAll(argv=None):
if argv is None:
argv = sys.argv
# Load an existing neuroConstruct project
projFile = File("../CElegans.ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
project = pm.loadProject(projFile)
print "Loaded project: " + project.getProjectName()
defSimConfig = project.simConfigInfo.getDefaultSimConfig()
cellsOnlySimConfig = project.simConfigInfo.getSimConfig("CellsOnly")
pharyngealSimConfig = project.simConfigInfo.getSimConfig("PharyngealNeurons")
mdl08SimConfig = project.simConfigInfo.getSimConfig("MDL08Connections")
expectedNumberCells = 302
##########################
print "\n----- Test 1: Check number of cells in sim config "+defSimConfig.getName()+"..."
pm.doGenerate(defSimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(defSimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
print "\n---- Test 2: number of cells in sim config "+cellsOnlySimConfig.getName()+"..."
pm.doGenerate(cellsOnlySimConfig.getName(), 1234)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(cellsOnlySimConfig)
sleep(2)
numGenerated = project.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
assert numGenerated == expectedNumberCells
print "Correct number of cells generated!"
##########################
filename = "../../CElegansNeuronTables.xls"
print "\n---- Test 3: confirm settings in project match those in "+filename+"..."
from xlrd import open_workbook
rb = open_workbook(filename)
print "Opened Excel file: "+ filename
confirmed = 0
prefix = "NCXLS_"
for row in range(1,rb.sheet_by_index(0).nrows):
pre = rb.sheet_by_index(0).cell(row,0).value
post = rb.sheet_by_index(0).cell(row,1).value
syntype = rb.sheet_by_index(0).cell(row,2).value
num = int(rb.sheet_by_index(0).cell(row,3).value)
synclass = rb.sheet_by_index(0).cell(row,4).value
#print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
netConnName = prefix+pre+"_"+post
if "GapJunction" in syntype:
netConnName = netConnName + "_GJ"
src = project.morphNetworkConnectionsInfo.getSourceCellGroup(netConnName)
tgt = project.morphNetworkConnectionsInfo.getTargetCellGroup(netConnName)
synlist = project.morphNetworkConnectionsInfo.getSynapseList(netConnName)
#print synlist
assert synclass == synlist[0].getSynapseType()
if '_GJ' in synclass and synclass != 'Generic_GJ':
print "Only allowed gap junction synapse is Generic_GJ, not "+synclass
assert synclass == 'Generic_GJ'
if not (src == pre and tgt == post):
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** Couldn't find connection: %s, src: %s, tgt: %s"%(netConnName, src, tgt)
assert src == pre
assert tgt == post
if src == tgt:
print "------------------------------------------\nConnection %i has %i from %s to %s (type: %s, synapse: %s)" %(row, num, pre, post, syntype, synclass)
print "*** This connection is from: %s, src: %s, tgt: %s, synaptic connection on same cell!!"%(netConnName, src, tgt)
confirmed += 1
print "Confirmed %i connections in project match spreadsheet"%confirmed
havePrefix = 0
allNetConnNames = project.morphNetworkConnectionsInfo.getAllSimpleNetConnNames()
for name in allNetConnNames:
if name.startswith(prefix):
havePrefix +=1
print "Project contains %i Network connections starting with %s"%(havePrefix, prefix)
assert havePrefix == confirmed
##########################
print "\n---- Test 4: number of cells in sim config "+pharyngealSimConfig.getName()+"..."
pm.doGenerate(pharyngealSimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(pharyngealSimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 20
expectedNetConns = 269
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 5: number of cells in sim config "+mdl08SimConfig.getName()+"..."
pm.doGenerate(mdl08SimConfig.getName(), 1234471)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(mdl08SimConfig)
sleep(2)
numCells = project.generatedCellPositions.getNumberInAllCellGroups()
numConns = project.generatedNetworkConnections.getNumAllSynConns()
print "Number of cells: %i, number of connections: %i"%(numCells,numConns)
expectedCells = 9
expectedNetConns = 21
assert numCells == expectedCells
assert numConns == expectedNetConns
print "Correct number of cells & connections generated!"
##########################
print "\n---- Test 6: General neuroConstruct project settings..."
assert(project.proj3Dproperties.getDisplayOption() == Display3DProperties.DISPLAY_SOMA_NEURITE_SOLID)
assert(abs(project.simulationParameters.getDt()-0.025)<=1e-9)
assert(not project.neuronSettings.isVarTimeStep())
assert(project.neuronSettings.getDataSaveFormat().equals(NeuronSettings.DataSaveFormat.TEXT_NC))
assert(abs(project.simulationParameters.getTemperature() - 20.0) < 1e-6)
##########################
print "\n------------------------------------------All tests completed!\n"
exit()
def setupLog4jLogging(trace=False, debug=False):
global log, logLevel
#coll_home = getCollHome()
#prog,ext = getProgramName()
#Load properties file in java.util.Properties
propsFileName = coll_home + "/etc/collation.properties"
inStream = FileInputStream(propsFileName)
propFile = Properties()
propFile.load(inStream)
if debug == True:
logLevel = "DEBUG"
else:
logLevel = System.getProperty("com.collation.log.level")
if logLevel == None:
logLevel = "Info"
# set properties for using the default TADDM log4j.xml file for logging
if System.getProperty("com.collation.log.level") == None:
System.setProperty("com.collation.log.level",
propFile.getProperty("com.collation.log.level"))
if System.getProperty("com.collation.log.filesize") == None:
System.setProperty("com.collation.log.filesize",
propFile.getProperty("com.collation.log.filesize"))
if System.getProperty("com.collation.log.filecount") == None:
System.setProperty("com.collation.log.filecount",
propFile.getProperty("com.collation.log.filecount"))
if System.getProperty("com.collation.log4j.servicename") == None:
System.setProperty("com.collation.log4j.servicename", "-" + prog)
#Start logging
# is a dedicated log4j.xml file provided (name is <prog>.xml
log4jFile = []
log4jFile.append("./" + prog + ".xml")
log4jFile.append(coll_home + "/etc/" + prog + ".xml")
log4jFile.append(coll_home + "/etc/log4j.xml")
for logF in log4jFile:
if os.path.isfile(logF):
log4j = logF
break
DOMConfigurator.configure(logF)
log = Logger.getLogger("com.ibm.cdb.TivoliStdMsgLogger")
layout = PatternLayout("%d{ISO8601} %X{service} [%t] %x %p %c{2} - %m\n")
if logLevel == "INFO":
log.setLevel(Level.INFO)
elif logLevel == "ERROR":
log.setLevel(Level.ERROR)
elif logLevel == "DEBUG":
log.setLevel(Level.DEBUG)
elif logLevel == "TRACE":
log.setLevel(Level.TRACE)
logfile = File(coll_home + "/log/" + prog + ".log")
fileAppender = FileAppender(layout, logfile.getAbsolutePath(), True)
log.addAppender(fileAppender)
if trace == True:
consoleAppender = ConsoleAppender(layout, "System.out")
log.addAppender(consoleAppender)
return log, logfile.getAbsolutePath()
simConfig.setSimDuration(simDuration)
for netConnName in simConfig.getNetConns():
if netConnName.count("gap")==0:
print "Changing synaptic delay in %s to %i"%(netConnName, defaultSynapticDelay)
delayGen = NumberGenerator(defaultSynapticDelay)
for synProps in myProject.morphNetworkConnectionsInfo.getSynapseList(netConnName):
synProps.setDelayGenerator(delayGen)
pm.doGenerate(simConfig.getName(), neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated with Simulation Configuration: "+str(simConfig)
sleep(1)
numGenerated = myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
myNetworkMLFile = File("TestNetwork.nml")
pm.saveNetworkStructureXML(myProject, myNetworkMLFile, 0, 0, simConfig.getName(), "Physiological Units")
print "Network structure saved to file: "+ myNetworkMLFile.getAbsolutePath()
quit()
from ucl.physiol.neuroconstruct.gui import SimulationRerunFrame
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
from math import *
import time
import shutil
import random
import os
import subprocess
# Load the original project
projName = "LarkumEtAl2009"
projFile = File("/home/matteo/neuroConstruct/models/"+projName+"/"+projName+".ncx")
print "Loading project from file: " + projFile.getAbsolutePath()+", exists: "+ str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
simConfig = myProject.simConfigInfo.getSimConfig("Default Simulation Configuration")#
randomseed = random.randint(1000,5000)
pm.doGenerate(simConfig.getName(), randomseed)
while pm.isGenerating():
print "Waiting for the project to be generated..."
time.sleep(2)
numGenerated = myProject.generatedCellPositions.getNumberInAllCellGroups()
simsRunning = []
def updateSimsRunning():
simsFinished = []
for sim in simsRunning:
timeFile = File(myProject.getProjectMainDirectory(), "simulations/"+sim+"/time.dat")
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from java.io import File
from ij import ImageJ, ImagePlus
from ij.io import Opener
from net.imglib2.img import Img, ImgFactory
from net.imglib2.img.cell import CellImgFactory
from net.imglib2.img.display.imagej import ImageJFunctions
from net.imglib2.type.numeric.real import FloatType
gitDir = os.environ['GIT_HOME']
relImg = "/OSImageAnalysis/images"
# strImg = gitDir + relImg + "/bridge.gif"
strImg = gitDir + relImg + "/latex.tif"
fi = File(strImg)
imp = Opener().openImage( fi.getAbsolutePath() )
imp.show()
imgFactory = CellImgFactory(5 )
img1 = imgFactory.create( (20, 30, 40), FloatType() )
ImageJFunctions.show( img1 )
img2 = imgFactory.create( img1, img1.firstElement() )
ImageJFunctions.show( img2 )
#
# Author: Padraig Gleeson
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellcome Trust
#
#
try:
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
file = File("../osb/showcase/neuroConstructShowcase/Ex1_Simple/Ex1_Simple.ncx")
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
myProject = pm.loadProject(file)
print pm.status()
# Remove this line to remain in interactive mode
System.exit(0)
for conn in connList:
nextWeight = random.random()
if conn.props is None:
csp = ConnSpecificProps(synProps.getSynapseType())
conn.props = ArrayList()
conn.props.add(csp)
conn.props.get(0).weight = nextWeight
print "Weight of one connection set to: %f" % nextWeight
myNetworkMLFile = File("TestNetwork.nml")
pm.saveNetworkStructureXML(myProject, myNetworkMLFile, 0, 0,
simConfig.getName(), "Physiological Units")
print "Network structure saved to file: " + myNetworkMLFile.getAbsolutePath()
if runInBackground:
myProject.neuronSettings.setNoConsole()
else:
myProject.neuronFileManager.setQuitAfterRun(1)
myProject.neuronFileManager.generateTheNeuronFiles(simConfig, None,
NeuronFileManager.RUN_HOC,
simulatorSeed)
print "Generated NEURON files for: " + simRef
compileProcess = ProcessManager(myProject.neuronFileManager.getMainHocFile())
compileSuccess = compileProcess.compileFileWithNeuron(0, 0)
#
# Author: Padraig Gleeson
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellcome Trust
#
#
try:
from java.io import File
from java.lang import System
except ImportError:
print "Note: this file should be run using ..\\nC.bat -python XXX.py' or './nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
from ucl.physiol.neuroconstruct.project import ProjectManager
file = File("../nCexamples/Ex1_Simple/Ex1_Simple.ncx")
print 'Loading project file: ', file.getAbsolutePath()
pm = ProjectManager()
myProject = pm.loadProject(file)
print pm.status()
# Remove this line to remain in interactive mode
System.exit(0)
# Author: Michael Sengelmann
import ghidra.app.script.GhidraScript
state = getState()
currentProgram = state.getCurrentProgram()
name = currentProgram.getName()
location = currentProgram.getExecutablePath()
# print("The currently loaded program is: '{}'".format(name))
# print("Its location on disk is: '{}'".format(location))
if (getProgramFile() is None):
print("File doesn't exist locally.")
from java.io import File
from javax.swing import JFileChooser
chooser = JFileChooser()
chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY)
chooser.setDialogTitle("Export " + name + " to...")
chooser.showDialog(None, None)
path = chooser.getSelectedFile().getAbsolutePath()
fullpath = path + "/" + name
f = File(fullpath)
print("Creating " + f.getAbsolutePath())
from ghidra.app.util.exporter import BinaryExporter
bexp = BinaryExporter()
memory = currentProgram.getMemory()
monitor = getMonitor()
domainObj = currentProgram
bexp.export(f, domainObj, memory, monitor)
else:
print("File already exists at " + getProgramFile().getAbsolutePath())
import os
try:
from java.io import File
except ImportError:
print "Note: this file should be run using nC.bat -python XXX.py' or 'nC.sh -python XXX.py'"
print "See http://www.neuroconstruct.org/docs/python.html for more details"
quit()
sys.path.append(os.environ["NC_HOME"]+"/pythonNeuroML/nCUtils")
import ncutils as nc
projFile = File(os.getcwd(), "../Ex10_NeuroML2.ncx")
print "Project file for this test: "+ projFile.getAbsolutePath()
############## Main settings ##################
simConfigs = []
simConfigs.append("Default Simulation Configuration")
simDt = 0.0005
#simulators = ["NEURON"]
simulators = ["NEURON", "LEMS"]
numConcurrentSims = 4
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
from ucl.physiol.neuroconstruct.simulation import SimulationData
from ucl.physiol.neuroconstruct.simulation import SpikeAnalyser
from math import *
import time
neuroConstructSeed = 1234
simulatorSeed = 4321
# Load an existing neuroConstruct project
projFile = File("TestPython/TestPython.neuro.xml")
print "Loading project from file: " + projFile.getAbsolutePath(
) + ", exists: " + str(projFile.exists())
pm = ProjectManager()
myProject = pm.loadProject(projFile)
simConfig = myProject.simConfigInfo.getSimConfig("SingleCell")
pm.doGenerate(simConfig.getName(), neuroConstructSeed)
while pm.isGenerating():
print "Waiting for the project to be generated..."
time.sleep(2)
numGenerated = myProject.generatedCellPositions.getNumberInAllCellGroups()
print "Number of cells generated: " + str(numGenerated)
