synchronize with commercial version 1.9.0

examples/IDC_Run/gdmlgen.py

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+#!/bin/env python
+import os
+import subprocess
+import time
+
+
+# genius install dir
+GENIUS_PATH = '/opt/cogenda/current/'
+
+
+def gdmlgen(source_file):
+  source_file = os.path.realpath(str(source_file))
+  file_dir = os.path.dirname(source_file)
+  file_name, file_ext = os.path.splitext(os.path.basename(source_file))
+
+  format = ''
+
+  if file_ext == '.unv' :
+    format = 'UNVFILE'
+
+  if file_ext == '.tif3d' :
+    format = 'TIF3DFILE'
+
+
+  params = {
+   'source_file':  source_file,
+   'gdml_file'  :  os.path.join(file_dir, file_name+'.gdml'),
+   'FORMAT'     :  format
+  }
+
+
+  tmpl_gdml=r'''
+  GLOBAL T=300 cm=1e5 second=1e-5
+  IMPORT {FORMAT:s}="{source_file:s}"
+  EXPORT GDML.SURFACE="{gdml_file:s}"
+  '''
+
+  inp_file = os.path.join(file_dir, 'gdml.inp')
+
+  with open(inp_file, 'w') as fout:
+      fout.write(tmpl_gdml.format(**params))
+
+  p = subprocess.Popen( [GENIUS_PATH + '/genius/bin/genius', '-i', inp_file])
+  out, err = p.communicate()
+
+
+#--------------------------------------
+# !!! user input !!!
+#--------------------------------------
+# source structure
+#source_file ='aa.unv'
+#gdmlgen(source_file)
+
+
+
+

examples/IDC_Run/gdmlgen_dlg.py

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+from gdmlgen import gdmlgen
+
+from PyQt4.QtCore import *
+from PyQt4.QtGui import *
+
+import os
+
+class gdmlgen_dlg(QDialog):
+
+    def __init__(self, parent=None):
+        super(gdmlgen_dlg, self).__init__(parent)
+
+        self.setWindowTitle(self.tr("gdml generator"))
+
+        vLayout = QVBoxLayout()
+        hLayout = QHBoxLayout()
+        hLayout.addWidget(QLabel(self.tr("3D Model File: ")))
+        self.leFPath = QLineEdit()
+        hLayout.addWidget(self.leFPath)
+        self.btFPath = QPushButton("...")
+        self.btFPath.setMaximumWidth(50)
+        self.btFPath.setMaximumHeight(25)
+        hLayout.addWidget(self.btFPath)
+        vLayout.addLayout(hLayout)
+
+        hLayout = QHBoxLayout()
+        self.btGdmlGen = QPushButton(self.tr("Generate GDML"))
+        self.btGdmlGen.setMaximumWidth(120)
+        hLayout.addWidget(self.btGdmlGen)
+        self.btCancle = QPushButton(self.tr("Cancle"))
+        self.btCancle.setMaximumWidth(120)
+        hLayout.addWidget(self.btCancle)
+        vLayout.addLayout(hLayout)
+
+        self.setLayout(vLayout)
+
+        self.resize(500, 100)
+
+        self.connect(self.btFPath, SIGNAL('clicked()'), self.onBtFPathClicked)
+        self.connect(self.btGdmlGen, SIGNAL('clicked()'), self.onbtGdmlGenClicked)
+        self.connect(self.btCancle, SIGNAL('clicked()'), self.reject)
+
+    def onBtFPathClicked(self):
+        homepath = QDir.homePath()
+        path = str( QFileDialog.getOpenFileName(self, self.tr("Open File"),\
+                                                homepath, self.tr("Model file(*.unv *.tif3d)")) )
+        if len(path)==0: return
+
+        self.leFPath.setText(path)
+
+    def onbtGdmlGenClicked(self):
+        path = str(self.leFPath.text())
+        if not os.path.isfile(path):
+            msg = self.tr("File '%s' does not exist"%path)
+            QMessageBox.warning(None, self.tr("File Error!"), msg)
+            return
+
+        gdmlgen(path)
+
+    def reject(self):
+        super(gdmlgen_dlg, self).reject()
+
+
+
+if __name__ == "__main__":
+    import sys
+    app = QApplication(sys.argv)
+    dlg = gdmlgen_dlg()
+
+    dlg.show()
+    app.exec_()

examples/IDC_Run/run.py

@@ -0,0 +1,81 @@
+#!/bin/env python
+import os
+import subprocess
+import time
+
+
+#--------------------------------------
+# !!! user input !!!
+#--------------------------------------
+
+
+# model file, UNV or TIF3D format
+#source_file ='aa.unv'
+
+# track of particle
+#track_file='t.dat'
+
+# position of inject particle
+#particle_file='p.dat'
+
+# weight of particle
+#weight=1.0
+
+# background mesh resolution, cm
+#resolution = 0.05
+
+# genius install dir
+GENIUS_PATH = '/opt/cogenda/current/'
+
+
+def run(source_file, track_file, particle_file, weight, resolution):
+  source_file = os.path.realpath(str(source_file))
+  file_dir = os.path.dirname(source_file)
+  file_name, file_ext = os.path.splitext(os.path.basename(source_file))
+
+  format = ''
+
+  if file_ext == '.unv' :
+    format = 'UNVFILE'
+
+  if file_ext == '.tif3d' :
+    format = 'TIF3DFILE'
+
+  result_file = os.path.join(file_dir, file_name+'.vtu')
+
+  params = {
+   'source_file':  source_file,
+   'FORMAT'     :  format,
+   'track_file' :  track_file,
+   'particle_file' : particle_file,
+   'weight'        : weight,
+   'result_file'   : result_file,
+   'resolution'    : resolution
+  }
+
+
+
+  tmpl_cmd=r'''
+  GLOBAL T=300 cm=1e5 second=1e-5
+  IMPORT {FORMAT:s}="{source_file:s}"
+
+  CONTACT Property=ElectrodeRegion Type=FixedPotential
+
+  METHOD Type=RIC NS=Basic LS=gmres pc=lu Damping=no toler.relax=1e5 maxit=25
+  HOOK   id=d1 Load=particle_capture_data  string<track.data>="{track_file:s}" string<particle.data>="{particle_file:s}"  \
+         real<weight>={weight:g}  real<resolution>={resolution:g}  real<fraction>=1
+
+  SOLVE Type=steadystate
+
+  # export result
+  EXPORT   VTKFILE="{result_file:s}"
+  '''
+
+  inp_file = os.path.join(file_dir, 'run.inp')
+
+  with open(inp_file, 'w') as fout:
+      fout.write(tmpl_cmd.format(**params))
+
+
+  p = subprocess.Popen( [GENIUS_PATH + '/genius/bin/genius', '-i', inp_file])
+  out, err = p.communicate()

examples/IDC_Run/run_dlg.py

@@ -0,0 +1,139 @@
+from run import run
+
+from PyQt4.QtCore import *
+from PyQt4.QtGui import *
+
+import os
+
+class run_dlg(QDialog):
+
+    def __init__(self, parent=None):
+        super(run_dlg, self).__init__(parent)
+
+        fvalidate = QDoubleValidator()
+        fvalidate.setNotation(QDoubleValidator.StandardNotation|
+                              QDoubleValidator.ScientificNotation)
+        fvalidate.setBottom(0)
+
+        self.setWindowTitle(self.tr("Run"))
+
+        vLayout = QVBoxLayout()
+        mLayout = QGridLayout()
+
+        mLayout.addWidget(QLabel(self.tr("Source file")), 0, 0)
+        self.leSrcFile = QLineEdit()
+        self.btSrcFile = QPushButton("...")
+        mLayout.addWidget(self.leSrcFile, 0, 1)
+        mLayout.addWidget(self.btSrcFile, 0, 2)
+
+        mLayout.addWidget(QLabel(self.tr("Track file")), 1, 0)
+        self.leTrkFile = QLineEdit()
+        self.btTrkFile = QPushButton("...")
+        mLayout.addWidget(self.leTrkFile, 1, 1)
+        mLayout.addWidget(self.btTrkFile, 1, 2)
+
+        mLayout.addWidget(QLabel(self.tr("Particle file")), 2, 0)
+        self.lePtkFile = QLineEdit()
+        self.btPtkFile = QPushButton("...")
+        mLayout.addWidget(self.lePtkFile, 2, 1)
+        mLayout.addWidget(self.btPtkFile, 2, 2)
+
+        mLayout.addWidget(QLabel(self.tr("Particle weight")), 3, 0)
+        self.lePtkWeight = QLineEdit("1.0")
+        self.lePtkWeight.setValidator(fvalidate)
+        self.lePtkWeight.setMaximumWidth(100)
+        mLayout.addWidget(self.lePtkWeight, 3, 1)
+
+        mLayout.addWidget(QLabel(self.tr("Grid resolution(mm)")), 4, 0)
+        self.leGridRslt = QLineEdit("0.05")
+        self.leGridRslt.setValidator(fvalidate)
+        self.leGridRslt.setMaximumWidth(100)
+        mLayout.addWidget(self.leGridRslt, 4, 1)
+
+        vLayout.addLayout(mLayout)
+
+        hLayout = QHBoxLayout()
+        self.btRun = QPushButton(self.tr("Run"))
+        self.btRun.setMaximumWidth(120)
+        hLayout.addWidget(self.btRun)
+        self.btCancle = QPushButton(self.tr("Cancle"))
+        self.btCancle.setMaximumWidth(120)
+        hLayout.addWidget(self.btCancle)
+        vLayout.addLayout(hLayout)
+
+        self.setLayout(vLayout)
+
+        self.resize(600, 200)
+
+        self.connect(self.btSrcFile, SIGNAL('clicked()'), self.onBtSrcFileClicked)
+        self.connect(self.btTrkFile, SIGNAL('clicked()'), self.onBtTrkFileClicked)
+        self.connect(self.btPtkFile, SIGNAL('clicked()'), self.onBtPtkFileClicked)
+        self.connect(self.btRun, SIGNAL('clicked()'), self.onBtRunClicked)
+        self.connect(self.btCancle, SIGNAL('clicked()'), self.reject)
+
+    def onBtSrcFileClicked(self):
+        homepath = QDir.homePath()
+        path = str( QFileDialog.getOpenFileName(self, self.tr("Open File"),\
+                                    homepath, self.tr("Model file(*.unv *.tif3d)")) )
+        if len(path)==0: return
+        self.leSrcFile.setText(path)
+
+    def onBtTrkFileClicked(self):
+        homepath = QDir.homePath()
+        path = str( QFileDialog.getOpenFileName(self, self.tr("Open File"),\
+                                    homepath, self.tr("Track file(*.*)")) )
+        if len(path)==0: return
+        self.leTrkFile.setText(path)
+
+    def onBtPtkFileClicked(self):
+        homepath = QDir.homePath()
+        path = str( QFileDialog.getOpenFileName(self, self.tr("Open File"),\
+                                    homepath, self.tr("Particle file(*.*)")) )
+        if len(path)==0: return
+        self.lePtkFile.setText(path)
+
+    def onBtRunClicked(self):
+        srcFile = str(self.leSrcFile.text())
+        if not os.path.isfile(srcFile):
+            msg = self.tr("Source File '%s' does not exist"%srcFile)
+            QMessageBox.warning(None, self.tr("File Error!"), msg)
+            return
+
+        trkFile = str(self.leTrkFile.text())
+        if not os.path.isfile(trkFile):
+            msg = self.tr("Track File '%s' does not exist"%trkFile)
+            QMessageBox.warning(None, self.tr("File Error!"), msg)
+            return
+
+        ptkFile = str(self.lePtkFile.text())
+        if not os.path.isfile(ptkFile):
+            msg = self.tr("Particle File '%s' does not exist"%ptkFile)
+            QMessageBox.warning(None, self.tr("File Error!"), msg)
+            return
+
+        ptkWeight = str(self.lePtkWeight.text())
+        if len(ptkWeight)==0:
+            msg = self.tr("Particle weight is not set")
+            return
+        ptkWeight = float(ptkWeight)
+
+        gridRslt = str(self.leGridRslt.text())
+        if len(gridRslt)==0:
+            msg = self.tr("Grid resolution is not set")
+            return
+        gridRslt = float(gridRslt)
+
+        run(srcFile, trkFile, ptkFile, ptkWeight, gridRslt)
+
+    def reject(self):
+        super(run_dlg, self).reject()
+
+
+
+if __name__ == "__main__":
+    import sys
+    app = QApplication(sys.argv)
+    dlg = run_dlg()
+
+    dlg.show()
+    app.exec_()