def run(in_dir, ou_dir, extension, minimum, maximum):
extension = extension.strip()
extension = "*" + extension
for path in glob(os.path.join(in_dir, '*.tif')):
print path + ':',
IJ.open(path)
imp = IJ.getImage()
minima = [x.strip() for x in ch_min.split(';')]
maxima = [x.strip() for x in ch_max.split(';')]
for c in range(0, imp.getNChannels()):
imp.setC(c + 1)
ip = imp.getProcessor()
stats = ip.getStats()
M = 2**ip.getBitDepth()
if minima[c] == '-1':
mi = stats.min
else:
mi = Double.parseDouble(minima[c])
if maxima[c] == '-1':
ma = stats.max
else:
ma = Double.parseDouble(maxima[c])
scale = M / (ma - mi)
ip.subtract(mi)
ip.multiply(scale)
print ' ch' + str(c) + '=[' + str(mi) + ' ... ' + str(ma) + ']',
print ' '
IJ.run('Make Composite')
IJ.run('RGB Color')
IJ.run('Save',
'save=[' + os.path.join(ou_dir, os.path.basename(path)) + ']')
IJ.run('Close All')
def XML_endElement(self, uri, localName, qName, sourceHandler):
try:
if (qName == SELM_Lagrangian.getSimpleName()):
#/* check all entries set */
x = 0
elif (qName == SELM_Lagrangian.tagXML_LagrangianName):
x = 0
elif (qName == SELM_Lagrangian.tagXML_LagrangianTypeStr):
x = 0
elif (qName == SELM_Lagrangian_CUSTOM1.tagXML_testVariable):
self.testVariable = Double.parseDouble(
self.xmlAttributes.getValue("value"))
print("WARNING: SELM_Lagrangian_CUSTOM1.py : XML_endElement()")
print("testVariable = " + str(self.testVariable))
except Exception, e:
self.exception_value = e
print("Error: SELM_Lagrangian_CUSTOM1.py : XML_endElement()")
if type(e) is java.lang.Exception:
print(e.getMessage())
e.printStackTrace()
else:
print(e)
def XML_endElement(self, uri, localName, qName, sourceHandler):
try:
if (qName == SELM_Eulerian.getSimpleName()):
#/* check all entries set */
x = 0;
elif (qName == SELM_Eulerian.tagXML_EulerianName):
x = 0;
elif (qName == SELM_Eulerian.tagXML_EulerianTypeStr):
x = 0;
elif (qName == SELM_Eulerian_CUSTOM1.tagXML_testVariable):
self.testVariable = Double.parseDouble(self.xmlAttributes.getValue("value"));
print("WARNING: SELM_Eulerian_CUSTOM1.py : XML_endElement()");
print("testVariable = " + str(self.testVariable));
except Exception, e:
self.exception_value = e;
print("Error: SELM_Eulerian_CUSTOM1.py : XML_endElement()");
if type(e) is java.lang.Exception:
print(e.getMessage());
e.printStackTrace();
else:
print(e);
def warn(self):
bboxString = self.textfield.getText()
if bboxString == "":
self.textfield.setBorder(self.defaultborder)
return
if len(bboxString.split(",")) != 4:
self.wrongEntry()
else:
for i, coordString in enumerate(bboxString.split(",")):
try:
coord = Double.parseDouble(coordString)
except NumberFormatException:
self.wrongEntry()
return
minmax = {0: (-180, 180), 1: (-90, 90),
2: (-180, 180), 3: (-90, 90)}
if not minmax[i][0] <= coord <= minmax[i][1]:
self.wrongEntry()
return
self.textfield.setBorder(self.defaultborder)
self.dlg.bboxPreviewTextField.setText(bboxString)
def warn(self):
bboxString = self.textfield.getText()
if bboxString == "":
self.textfield.setBorder(self.defaultborder)
return
if len(bboxString.split(",")) != 4:
self.wrongEntry()
else:
for i, coordString in enumerate(bboxString.split(",")):
try:
coord = Double.parseDouble(coordString)
except NumberFormatException:
self.wrongEntry()
return
minmax = {0: (-180, 180), 1: (-90, 90),
2: (-180, 180), 3: (-90, 90)}
if not minmax[i][0] <= coord <= minmax[i][1]:
self.wrongEntry()
return
self.textfield.setBorder(self.defaultborder)
self.dlg.bboxPreviewTextField.setText(bboxString)
def stringToDouble(value):
return Double.parseDouble(value.strip())
def stringToDouble(value): return Double.parseDouble(value.strip())
def parameterScan():
global scan_device_server_name
global scan_1d_front
global scan_2d_front
global path
global data_file
global file_extension
global actuators
global sensors
global n_steps
global integration_time
global start_position_actuators_1D
global end_position_actuators_1D
global n_steps2
global start_position_actuators_2D
global end_position_actuators_2D
global timebase
global scan_number
global scan_type
global has_trajectory
global file_path
global actuators2D
#open the file in read only mode
#file = DataInputStream(FileInputStream("D:\eclipse\workspace\passerelle-soleil\sample-models\paramscan.txt"))
file = open(file_path,'r')
parameters = {}
for line in file.readlines():
#print "line ",line
tokens = line.split('=')
#print "tokens ",tokens
if(len(tokens) == 2):
tok0 = String(tokens[0])
tok1 = String(tokens[1])
tok0 = tok0.trim()
tok1 = tok1.trim()
parameters[tok0] = tok1
print tok0,":",tok1
if(parameters.has_key("scan_device_server_name")):
scan_device_server_name = parameters["scan_device_server_name"]
if(parameters.has_key("scan_1d_front")):
scan_1d_front = parameters["scan_1d_front"]
if(parameters.has_key("scan_2d_front")):
scan_2d_front = parameters["scan_2d_front"]
if(parameters.has_key("path")):
path = parameters["path"]
if(parameters.has_key("data_file")):
data_file = parameters["data_file"]
if(parameters.has_key("file_extension")):
file_extension = parameters["file_extension"]
if(parameters.has_key("actuators")):
actuators = parameters["actuators"].split(",")
#print "parameterScan actuators ",parameters["actuators"].split(",")
if(parameters.has_key("sensors")):
sensors = parameters["sensors"].split(",")
#if(parameters.has_key("n_steps")):
#n_steps = Integer.parseInt(parameters["n_steps"])
#if(parameters.has_key("integration_time")):
#integration_time = Double.parseDouble(parameters["integration_time"])
#if(parameters.has_key("start_position_actuators_1D")):
# stringTable = parameters["start_position_actuators_1D"].split(",")
# start_position_actuators_1D = []
# for i in stringTable:
# start_position_actuators_1D.append(Double.parseDouble(i))
if(parameters.has_key("end_position_actuators_1D")):
stringTable = parameters["end_position_actuators_1D"].split(",")
end_position_actuators_1D = []
for i in stringTable:
end_position_actuators_1D.append(Double.parseDouble(i))
if(parameters.has_key("actuators2D")):
actuators2D = parameters["actuators2D"].split(",")
#print "parameterScan actuators ",parameters["actuators"].split(",")
if(parameters.has_key("n_steps2")):
n_steps2 = Integer.parseInt(parameters["n_steps2"])
if(parameters.has_key("start_position_actuators_2D")):
stringTable = parameters["start_position_actuators_2D"].split(",")
start_position_actuators_2D = []
for i in stringTable:
start_position_actuators_2D.append(Double.parseDouble(i))
if(parameters.has_key("end_position_actuators_2D")):
stringTable = parameters["end_position_actuators_2D"].split(",")
end_position_actuators_2D = []
for i in stringTable:
end_position_actuators_2D.append(Double.parseDouble(i))
if(parameters.has_key("timebase")):
timebase = parameters["timebase"]
if(parameters.has_key("scan_number")):
scan_number = Integer.parseInt(parameters["scan_number"])
if(parameters.has_key("scan_type")):
scan_type = Integer.parseInt(parameters["scan_type"])
if(parameters.has_key("has_trajectory")):
has_trajectory = Integer.parseInt(parameters["has_trajectory"])
message = container.getInputMessage(0)
messageBody = message.getBodyContentAsString()
#if inputPortNr == 0:
print "input 0: ",messageBody
file_path = messageBody
message = container.getInputMessage(1)
messageBody = Long.parseLong(message.getBodyContentAsString())
#if inputPortNr == 1:
print "input 1: ",messageBody
n_steps = messageBody
message = container.getInputMessage(2)
messageBody = Double.parseDouble(message.getBodyContentAsString())
print "input 2: ",messageBody
integration_time = messageBody
message = container.getInputMessage(3)
messageBody = message.getBodyContentAsString()
print "input 3: ",messageBody
stringTable = messageBody.split(",")
start_position_actuators_1D = []
for i in stringTable:
start_position_actuators_1D.append(Double.parseDouble(i))
#===============================================
# Get all parameters from file
#===============================================
parameterScan()
def _getIndex(self, even, odd):
mergePolicy = LogDocMergePolicy()
mergePolicy.setMergeFactor(1000)
directory = RAMDirectory()
self.dirs.append(directory)
writer = self.getWriter(directory=directory,
analyzer=SimpleAnalyzer(Version.LUCENE_CURRENT),
maxBufferedDocs=2, mergePolicy=mergePolicy)
if self.dvStringSorted:
# Index sorted
stringDVType = FieldInfo.DocValuesType.SORTED
elif self.notSorted:
# Index non-sorted
stringDVType = FieldInfo.DocValuesType.BINARY
else:
# sorted anyway
stringDVType = FieldInfo.DocValuesType.SORTED
ft1 = FieldType()
ft1.setStored(True)
ft2 = FieldType()
ft2.setIndexed(True)
for i in xrange(len(self.data)):
if (i % 2 == 0 and even) or (i % 2 == 1 and odd):
doc = Document()
doc.add(Field("tracer", self.data[i][0], ft1))
doc.add(TextField("contents", self.data[i][1], Field.Store.NO))
if self.data[i][2] is not None:
doc.add(StringField("int", self.data[i][2], Field.Store.NO))
if self.supportsDocValues:
doc.add(NumericDocValuesField("int_dv", Long.parseLong(self.data[i][2])))
if self.data[i][3] is not None:
doc.add(StringField("float", self.data[i][3], Field.Store.NO))
if self.supportsDocValues:
doc.add(FloatDocValuesField("float_dv", Float.parseFloat(self.data[i][3])))
if self.data[i][4] is not None:
doc.add(StringField("string", self.data[i][4], Field.Store.NO))
if self.supportsDocValues:
if stringDVType == FieldInfo.DocValuesType.SORTED:
doc.add(SortedDocValuesField("string_dv", BytesRef(self.data[i][4])))
elif stringDVType == FieldInfo.DocValuesType.BINARY:
doc.add(BinaryDocValuesField("string_dv", BytesRef(self.data[i][4])))
else:
raise ValueError("unknown type " + stringDVType)
if self.data[i][5] is not None:
doc.add(StringField("custom", self.data[i][5], Field.Store.NO))
if self.data[i][6] is not None:
doc.add(StringField("i18n", self.data[i][6], Field.Store.NO))
if self.data[i][7] is not None:
doc.add(StringField("long", self.data[i][7], Field.Store.NO))
if self.data[i][8] is not None:
doc.add(StringField("double", self.data[i][8], Field.Store.NO))
if self.supportsDocValues:
doc.add(NumericDocValuesField("double_dv", Double.doubleToRawLongBits(Double.parseDouble(self.data[i][8]))))
if self.data[i][9] is not None:
doc.add(StringField("short", self.data[i][9], Field.Store.NO))
if self.data[i][10] is not None:
doc.add(StringField("byte", self.data[i][10], Field.Store.NO))
if self.data[i][11] is not None:
doc.add(StringField("parser", self.data[i][11], Field.Store.NO))
for f in doc.getFields():
if f.fieldType().indexed() and not f.fieldType().omitNorms():
Field.cast_(f).setBoost(2.0)
writer.addDocument(doc)
reader = writer.getReader()
writer.close()
return self.getSearcher(reader=reader)
import be.isencia.passerelle.message.MessageFactory as MessageFactory import java.lang.Double as Double import java.lang.reflect.Array as Array import be.isencia.passerelle.message.ManagedMessage as ManagedMessage # get content of port 0 message = container.getInputMessage(0) messageBody = message.getBodyContent() print "Message: ", messageBody #process content of input test = range(messageBody.__len__()) test[0] = 12 print test test[0] = Double.parseDouble(messageBody[0]) j=0 while j < messageBody.__len__(): test[j] = Double.parseDouble(messageBody[j]) j = j+1 print test i=0 while i < messageBody.__len__(): test[i] = test[i]+1 i = i+1 array(test, Double) print test #put result in a passerelle message
