def resultsToDict(self):
"""Extracts all important results into dictionary, making
it easier for printout or csv extraction.
"""
parms=["DOptMu","DOptPx","prodOpt","degrOpt","success","Rsq","MeanRsq","fitDegr","fitProd","fitPinned","equOn","x0"]
dic=pyfrp_misc_module.objAttr2Dict(self,attr=parms)
roiNames=pyfrp_misc_module.objAttrToList(self.ROIsFitted,"name")
#equFacts=np.asarray(self.equFacts).astype(str)
dic["ROIsFitted"]=" , ".join(roiNames)
for i in range(len(roiNames)):
if self.equOn:
dic["equFactor "+roiNames[i]]=self.equFacts[i]
else:
dic["equFactor "+roiNames[i]]=""
dic["Rsq("+roiNames[i]+")"]=self.RsqByROI[roiNames[i]]
return dic
def getAttrFromROI(self, attr):
"""First finds all ROIs in ``geometry.embryo.ROIs`` that
have an attribute called ``attr``, then lets the user
select one of them and then returns the value of
``attr`` of the selected ROI.
"""
possROIs = list(self.geometry.embryo.ROIs)
possROIsNew = []
for r in possROIs:
if hasattr(r, attr):
possROIsNew.append(r)
possROIs = list(possROIsNew)
if len(possROIs) < 1:
printWarning(
"Cannot create selection of ROIs, there is none with attribute "
+ attr + " .")
return None
nameList = pyfrp_misc_module.objAttrToList(possROIs, 'name')
selectorDialog = pyfrp_gui_basics.basicSelectorDialog(nameList, self)
if selectorDialog.exec_():
selectedROIName = selectorDialog.getItem()
if selectedROIName == None:
return None
r = self.geometry.embryo.getROIByName(selectedROIName)
attrVal = getattr(r, attr)
return attrVal
def resultsToDict(self):
"""Extracts all important results into dictionary, making
it easier for printout or csv extraction.
"""
parms = [
"DOptMu", "DOptPx", "prodOpt", "degrOpt", "success", "Rsq",
"MeanRsq", "fitDegr", "fitProd", "fitPinned", "equOn", "x0"
]
dic = pyfrp_misc_module.objAttr2Dict(self, attr=parms)
roiNames = pyfrp_misc_module.objAttrToList(self.ROIsFitted, "name")
#equFacts=np.asarray(self.equFacts).astype(str)
dic["ROIsFitted"] = " , ".join(roiNames)
for i in range(len(roiNames)):
if self.equOn:
dic["equFactor " + roiNames[i]] = self.equFacts[i]
else:
dic["equFactor " + roiNames[i]] = ""
dic["Rsq(" + roiNames[i] + ")"] = self.RsqByROI[roiNames[i]]
return dic
def getAttrFromROI(self,attr):
"""First finds all ROIs in ``geometry.embryo.ROIs`` that
have an attribute called ``attr``, then lets the user
select one of them and then returns the value of
``attr`` of the selected ROI.
"""
possROIs=list(self.geometry.embryo.ROIs)
possROIsNew=[]
for r in possROIs:
if hasattr(r,attr):
possROIsNew.append(r)
possROIs=list(possROIsNew)
if len(possROIs)<1:
printWarning("Cannot create selection of ROIs, there is none with attribute " + attr + " .")
return None
nameList=pyfrp_misc_module.objAttrToList(possROIs,'name')
selectorDialog = pyfrp_gui_basics.basicSelectorDialog(nameList,self)
if selectorDialog.exec_():
selectedROIName = selectorDialog.getItem()
if selectedROIName==None:
return None
r=self.geometry.embryo.getROIByName(selectedROIName)
attrVal=getattr(r,attr)
return attrVal
def updateNormROILbl(self): nameList=pyfrp_misc_module.objAttrToList(self.embryo.ROIs,'name') if self.normName in nameList: pass else: self.normName="" self.lblNormVal.setText(self.normName)
def updateBkgdROILbl(self):
nameList = pyfrp_misc_module.objAttrToList(self.embryo.ROIs, 'name')
if self.bkgdName in nameList:
pass
else:
self.bkgdName = ""
self.lblBkgdVal.setText(self.bkgdName)
def updateNormROILbl(self):
nameList = pyfrp_misc_module.objAttrToList(self.embryo.ROIs, 'name')
if self.normName in nameList:
pass
else:
self.normName = ""
self.lblNormVal.setText(self.normName)
def updateBkgdROILbl(self): nameList=pyfrp_misc_module.objAttrToList(self.embryo.ROIs,'name') if self.bkgdName in nameList: pass else: self.bkgdName="" self.lblBkgdVal.setText(self.bkgdName)
def __init__(self,embryo,parent):
super(boundaryLayerAroundROISettingsDialog,self).__init__(parent)
# Set default variables
self.embryo=embryo
self.initDefaults()
# Generate all widgets
self.lblSegments,self.qleSegments = pyfrp_gui_builder.genSettingQLE(self,"Segments",self.segments,callback=self.setSegments,validator=self.intValid)
self.lblIter,self.qleIter = pyfrp_gui_builder.genSettingQLE(self,"Iterations",self.iterations,callback=self.setIter,validator=self.intValid)
self.lblTriangIter,self.qleTriangIter = pyfrp_gui_builder.genSettingQLE(self,"triangIterations",self.triangIterations,callback=self.setTriangIter,validator=self.intValid)
self.lblVolSizePx,self.qleVolSizePx = pyfrp_gui_builder.genSettingQLE(self,"volSizePx",self.volSizePx,callback=self.setVolSizePx,validator=self.doubleValid)
self.lblVolSizeLayer,self.qleVolSizeLayer = pyfrp_gui_builder.genSettingQLE(self,"volSizeLayer",self.volSizeLayer,callback=self.setVolSizeLayer,validator=self.doubleValid)
self.lblThickness,self.qleThickness = pyfrp_gui_builder.genSettingQLE(self,"thickness",self.thickness,callback=self.setThickness,validator=self.doubleValid)
self.lblAngleThresh,self.qleAngleThresh = pyfrp_gui_builder.genSettingQLE(self,"angleThresh",self.angleThresh,callback=self.setAngleThresh,validator=self.doubleValid)
self.lblFaces,self.qleFaces = pyfrp_gui_builder.genSettingQLE(self,"Faces",self.faces,callback=self.setFaces,validator=None)
self.lblFnOut,self.btnFnOut = pyfrp_gui_builder.genSettingBtn(self,"fnOut","Change",callback=self.setFnOut)
self.lblOnlyAbs,self.cbOnlyAbs = pyfrp_gui_builder.genSettingCB(self,"onlyAbs",self.onlyAbs,callback=self.checkOnlyAbs)
self.lblSimplify,self.cbSimplify = pyfrp_gui_builder.genSettingCB(self,"simplify",self.simplify,callback=self.checkSimplify)
self.lblFixSurf,self.cbFixSurf = pyfrp_gui_builder.genSettingCB(self,"fixSurfaces",self.fixSurfaces,callback=self.checkFixSurf)
self.lblApproxBySpline,self.cbApproxBySpline = pyfrp_gui_builder.genSettingCB(self,"approxBySpline",self.approxBySpline,callback=self.checkApproxBySpline)
self.lblDebug,self.cbDebug = pyfrp_gui_builder.genSettingCB(self,"debug",self.debug,callback=self.checkDebug)
self.lblCleanUp,self.cbCleanUp = pyfrp_gui_builder.genSettingCB(self,"cleanUp",self.cleanUp,callback=self.checkCleanUp)
self.lblROI,self.comboROI = pyfrp_gui_builder.genSettingCombo(self,"ROI",pyfrp_misc_module.objAttrToList(self.embryo.ROIs,"name"),callback=self.setROI,idx=self.embryo.getROIIdx(self.roiUsed))
# Put them in list
lbls1 = [self.lblROI,self.lblFaces,self.lblOnlyAbs,self.lblFnOut]
qles1 = [self.comboROI,self.qleFaces,self.cbOnlyAbs,self.btnFnOut]
lbls2 = [self.lblVolSizePx,self.lblVolSizeLayer,self.lblThickness]
qles2 = [self.qleVolSizePx,self.qleVolSizeLayer,self.qleThickness]
lbls3 = [self.lblSegments,self.lblIter,self.lblTriangIter]
qles3 = [self.qleSegments,self.qleIter,self.qleTriangIter]
lbls4 = [self.lblSimplify,self.lblFixSurf,self.lblApproxBySpline,self.lblAngleThresh]
qles4 = [self.cbSimplify,self.cbFixSurf,self.cbApproxBySpline,self.qleAngleThresh]
lbls5 = [self.lblDebug,self.lblCleanUp]
qles5 = [self.cbDebug,self.cbCleanUp]
lbls=[lbls1,lbls2,lbls3,lbls4,lbls5]
qles=[qles1,qles2,qles3,qles4,qles5]
# Add to Layout
nRows=self.grid.rowCount()
for i in range(len(lbls)):
for j in range(len(lbls[i])):
self.grid.addWidget(lbls[i][j],nRows+j+1,(2*i))
self.grid.addWidget(qles[i][j],nRows+j+1,(2*i+1))
self.setWindowTitle("Boundary Layer Mesh around ROI settings")
self.show()
def setNormROI(self): nameList=pyfrp_misc_module.objAttrToList(self.embryo.ROIs,'name') selectorDialog = pyfrp_gui_basics.basicSelectorDialog(nameList,self) if selectorDialog.exec_(): selectedROIName = selectorDialog.getItem() if selectedROIName==None: return self.normName=selectedROIName self.updateNormROILbl()
def setNormROI(self):
nameList = pyfrp_misc_module.objAttrToList(self.embryo.ROIs, 'name')
selectorDialog = pyfrp_gui_basics.basicSelectorDialog(nameList, self)
if selectorDialog.exec_():
selectedROIName = selectorDialog.getItem()
if selectedROIName == None:
return
self.normName = selectedROIName
self.updateNormROILbl()
def sumUpResults(self, sameSettings=False):
"""Sums up results from all fits in ``selFits`` list.
Keyword Args:
sameSettings (bool): Fits must overlap in parameters defined in ``crucialParameters``.
Returns:
bool: True if success, False else.
"""
if sameSettings:
lastFit = self.selFits[0]
#Check that all fits have roughly the same parameters
for fit in self.selFits:
#Check if fit is fitted
if not fit.isFitted():
printError("Cannot average fits, since fits " + fit.name +
"has not been fitted yet.")
return False
same, different, notInBoth = pyfrp_misc_module.compareObjAttr(
lastFit, fit)
for item in self.crucialParameters:
if item in different.keys():
printError(
"Cannot average fits, since fits " + lastFit.name +
" and " + fit.name +
"do not have the same value for " + item +
". However, this parameter is marked as crucial.")
return False
elif item in notInBoth:
printError(
"Cannot average fits, since one of the fits " +
lastFit.name + " and " + fit.name +
" lacks the parameter " + item + ".")
return False
#Compute Statistics
self.DOptMu, self.DOptMuStd, self.DOptMuSterr = pyfrp_stats_module.parameterStats(
pyfrp_misc_module.objAttrToList(self.selFits, "DOptMu"))
self.DOptPx, self.DOptPxStd, self.DOptPxSterr = pyfrp_stats_module.parameterStats(
pyfrp_misc_module.objAttrToList(self.selFits, "DOptPx"))
self.prodOpt, self.prodOptStd, self.prodOptSterr = pyfrp_stats_module.parameterStats(
pyfrp_misc_module.objAttrToList(self.selFits, "prodOpt"))
self.degrOpt, self.degrOptStd, self.degrOptSterr = pyfrp_stats_module.parameterStats(
pyfrp_misc_module.objAttrToList(self.selFits, "degrOpt"))
self.Rsq = np.mean(pyfrp_misc_module.objAttrToList(
self.selFits, "Rsq"))
self.MeanRsq = np.mean(
pyfrp_misc_module.objAttrToList(self.selFits, "MeanRsq"))
return True
def checkEmbryoNames(self):
"""Check if all embryos in ``embryos`` list have different names.
Returns:
bool: True if all different, False else.
"""
names = pyfrp_misc_module.objAttrToList(self.embryos, 'name')
b = True
for name in names:
if names.count(name) > 1:
printWarning('There is more than one embryo called ' + name +
' in molecule ' + self.name)
b = False
return b
def checkEmbryoNames(self):
"""Check if all embryos in ``embryos`` list have different names.
Returns:
bool: True if all different, False else.
"""
names=pyfrp_misc_module.objAttrToList(self.embryos,'name')
b=True
for name in names:
if names.count(name)>1:
printWarning('There is more than one embryo called '+ name + ' in molecule ' + self.name)
b=False
return b
def addROI(self): nameList=pyfrp_misc_module.objAttrToList(self.fit.embryo.ROIs,'name') selectorDialog = pyfrp_gui_basics.basicSelectorDialog(nameList,self) if selectorDialog.exec_(): selectedROIName = selectorDialog.getItem() if selectedROIName==None: return selectedROI=self.fit.embryo.ROIs[nameList.index(selectedROIName)] if selectedROI not in self.fit.ROIsFitted: self.fit.addROI(selectedROI) self.updateROIList()
def test_surfaceFuse(): """Test surface fuse function. Reads in .stl, tries to fuse a few surfaces and checks if new surface lineLoop has proper number of vertices.""" d=pyfrp_gmsh_IO_module.readStlFile(pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir()+"tests/surfaceFuse.stl")) sfID=1 toFuseIDs=[2,3,4,5,6,7] # Grab first surface sf1=d.getRuledSurfaceById(sfID)[0] # Try to successively fuse for ID in toFuseIDs: sf1.fuse(d.getRuledSurfaceById(ID)[0],debug=True) assert pyfrp_misc_module.objAttrToList(sf1.lineLoop.getVertices(),'Id') == [1, 2, 4, 5, 6, 7, 8, 9, 3]
def test_surfaceFuse():
"""Test surface fuse function.
Reads in .stl, tries to fuse a few surfaces and checks if new surface
lineLoop has proper number of vertices."""
d = pyfrp_gmsh_IO_module.readStlFile(
pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir() +
"tests/surfaceFuse.stl"))
sfID = 1
toFuseIDs = [2, 3, 4, 5, 6, 7]
# Grab first surface
sf1 = d.getRuledSurfaceById(sfID)[0]
# Try to successively fuse
for ID in toFuseIDs:
sf1.fuse(d.getRuledSurfaceById(ID)[0], debug=True)
assert pyfrp_misc_module.objAttrToList(
sf1.lineLoop.getVertices(), 'Id') == [1, 2, 4, 5, 6, 7, 8, 9, 3]
def sumUpResults(self,sameSettings=False):
"""Sums up results from all fits in ``selFits`` list.
Keyword Args:
sameSettings (bool): Fits must overlap in parameters defined in ``crucialParameters``.
Returns:
bool: True if success, False else.
"""
if sameSettings:
lastFit=self.selFits[0]
#Check that all fits have roughly the same parameters
for fit in self.selFits:
#Check if fit is fitted
if not fit.isFitted():
printError("Cannot average fits, since fits " + fit.name + "has not been fitted yet.")
return False
same,different,notInBoth=pyfrp_misc_module.compareObjAttr(lastFit,fit)
for item in self.crucialParameters:
if item in different.keys():
printError("Cannot average fits, since fits " + lastFit.name + " and " + fit.name + "do not have the same value for " + item +". However, this parameter is marked as crucial.")
return False
elif item in notInBoth:
printError("Cannot average fits, since one of the fits " + lastFit.name + " and " + fit.name + " lacks the parameter " + item +".")
return False
#Compute Statistics
self.DOptMu,self.DOptMuStd,self.DOptMuSterr=pyfrp_stats_module.parameterStats(pyfrp_misc_module.objAttrToList(self.selFits,"DOptMu"))
self.DOptPx,self.DOptPxStd,self.DOptPxSterr=pyfrp_stats_module.parameterStats(pyfrp_misc_module.objAttrToList(self.selFits,"DOptPx"))
self.prodOpt,self.prodOptStd,self.prodOptSterr=pyfrp_stats_module.parameterStats(pyfrp_misc_module.objAttrToList(self.selFits,"prodOpt"))
self.degrOpt,self.degrOptStd,self.degrOptSterr=pyfrp_stats_module.parameterStats(pyfrp_misc_module.objAttrToList(self.selFits,"degrOpt"))
self.Rsq=np.mean(pyfrp_misc_module.objAttrToList(self.selFits,"Rsq"))
self.MeanRsq=np.mean(pyfrp_misc_module.objAttrToList(self.selFits,"MeanRsq"))
return True
def __init__(self, embryo, parent):
super(boundaryLayerAroundROISettingsDialog, self).__init__(parent)
# Set default variables
self.embryo = embryo
self.initDefaults()
# Generate all widgets
self.lblSegments, self.qleSegments = pyfrp_gui_builder.genSettingQLE(
self,
"Segments",
self.segments,
callback=self.setSegments,
validator=self.intValid)
self.lblIter, self.qleIter = pyfrp_gui_builder.genSettingQLE(
self,
"Iterations",
self.iterations,
callback=self.setIter,
validator=self.intValid)
self.lblTriangIter, self.qleTriangIter = pyfrp_gui_builder.genSettingQLE(
self,
"triangIterations",
self.triangIterations,
callback=self.setTriangIter,
validator=self.intValid)
self.lblVolSizePx, self.qleVolSizePx = pyfrp_gui_builder.genSettingQLE(
self,
"volSizePx",
self.volSizePx,
callback=self.setVolSizePx,
validator=self.doubleValid)
self.lblVolSizeLayer, self.qleVolSizeLayer = pyfrp_gui_builder.genSettingQLE(
self,
"volSizeLayer",
self.volSizeLayer,
callback=self.setVolSizeLayer,
validator=self.doubleValid)
self.lblThickness, self.qleThickness = pyfrp_gui_builder.genSettingQLE(
self,
"thickness",
self.thickness,
callback=self.setThickness,
validator=self.doubleValid)
self.lblAngleThresh, self.qleAngleThresh = pyfrp_gui_builder.genSettingQLE(
self,
"angleThresh",
self.angleThresh,
callback=self.setAngleThresh,
validator=self.doubleValid)
self.lblFaces, self.qleFaces = pyfrp_gui_builder.genSettingQLE(
self, "Faces", self.faces, callback=self.setFaces, validator=None)
self.lblFnOut, self.btnFnOut = pyfrp_gui_builder.genSettingBtn(
self, "fnOut", "Change", callback=self.setFnOut)
self.lblOnlyAbs, self.cbOnlyAbs = pyfrp_gui_builder.genSettingCB(
self, "onlyAbs", self.onlyAbs, callback=self.checkOnlyAbs)
self.lblSimplify, self.cbSimplify = pyfrp_gui_builder.genSettingCB(
self, "simplify", self.simplify, callback=self.checkSimplify)
self.lblFixSurf, self.cbFixSurf = pyfrp_gui_builder.genSettingCB(
self, "fixSurfaces", self.fixSurfaces, callback=self.checkFixSurf)
self.lblApproxBySpline, self.cbApproxBySpline = pyfrp_gui_builder.genSettingCB(
self,
"approxBySpline",
self.approxBySpline,
callback=self.checkApproxBySpline)
self.lblDebug, self.cbDebug = pyfrp_gui_builder.genSettingCB(
self, "debug", self.debug, callback=self.checkDebug)
self.lblCleanUp, self.cbCleanUp = pyfrp_gui_builder.genSettingCB(
self, "cleanUp", self.cleanUp, callback=self.checkCleanUp)
self.lblROI, self.comboROI = pyfrp_gui_builder.genSettingCombo(
self,
"ROI",
pyfrp_misc_module.objAttrToList(self.embryo.ROIs, "name"),
callback=self.setROI,
idx=self.embryo.getROIIdx(self.roiUsed))
# Put them in list
lbls1 = [self.lblROI, self.lblFaces, self.lblOnlyAbs, self.lblFnOut]
qles1 = [self.comboROI, self.qleFaces, self.cbOnlyAbs, self.btnFnOut]
lbls2 = [self.lblVolSizePx, self.lblVolSizeLayer, self.lblThickness]
qles2 = [self.qleVolSizePx, self.qleVolSizeLayer, self.qleThickness]
lbls3 = [self.lblSegments, self.lblIter, self.lblTriangIter]
qles3 = [self.qleSegments, self.qleIter, self.qleTriangIter]
lbls4 = [
self.lblSimplify, self.lblFixSurf, self.lblApproxBySpline,
self.lblAngleThresh
]
qles4 = [
self.cbSimplify, self.cbFixSurf, self.cbApproxBySpline,
self.qleAngleThresh
]
lbls5 = [self.lblDebug, self.lblCleanUp]
qles5 = [self.cbDebug, self.cbCleanUp]
lbls = [lbls1, lbls2, lbls3, lbls4, lbls5]
qles = [qles1, qles2, qles3, qles4, qles5]
# Add to Layout
nRows = self.grid.rowCount()
for i in range(len(lbls)):
for j in range(len(lbls[i])):
self.grid.addWidget(lbls[i][j], nRows + j + 1, (2 * i))
self.grid.addWidget(qles[i][j], nRows + j + 1, (2 * i + 1))
self.setWindowTitle("Boundary Layer Mesh around ROI settings")
self.show()
def addBoundaryLayerAroundROI(self,
roi,
fnOut=None,
segments=48,
simplify=True,
iterations=3,
triangIterations=2,
fixSurfaces=True,
debug=False,
volSizePx=None,
volSizeLayer=10,
thickness=15.,
cleanUp=True,
approxBySpline=True,
angleThresh=0.95,
faces='all',
onlyAbs=True):
"""Adds boundary layer around ROI to the mesh.
Does this by:
* Generating a stl file describing ROI, see also :py:func:`pyfrp.subclasses.pyfrp_ROI.ROI.render2StlInGeometry`.
* Read in stl file as new :py:class:`pyfrp.modules.pyfrp_gmsh_geometry.domain` via
:py:func:`pyfrp.modules.pyfrp_gmsh_IO_module.readStlFile`.
* Simplify new geometry via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.simplifySurfaces`.
* Extracting selected surfaces via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.gmshElement.extract`.
* If selected, surface boundaries are approximated into splines via
:py:func:`pyfrp.modules.pyfrp_gmsh_geometry.gmshElement.extract`.
* Reading in geometry's .geo file via :py:func:`pyfrp.sublcasses.pyfrp_geometry.geometry.readGeoFile`.
* Merging ROI geometry into main geometry via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.merge`.
* Adding a boundary layer mesh via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.addBoundaryLayerField`.
* Adding all surfaces of ROI's domain to boundary layer, see
:py:func:`pyfrp.modules.pyfrp_gmsh_geometry.boundaryLayerField.addFaceListByID`.
* Writing new .geo file.
* Setting new .geo file as ``fnGeo``.
* Running :py:func:`genMesh`.
* Clean up .stl and .scad files that are not needed anymore.
.. note:: ``volSizeLayer`` only allows a single definition of mesh size in layer. Note that the
:py:class:`pyfrp.modules.pyfrp_gmsh_geometry.boundaryLayerField` class allows different mesh sizes
normal and along surfaces. For more information, see its documentation.
.. note:: If no ``fnOut`` is given, will save a new .geo file in same folder as original ``fnGeo`` with subfix:
``fnGeo_roiName_BL.geo``.
.. note:: :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.simplifySurfaces` is not a simple procedure,
we recommend reading its documentation.
If ``volSizePx`` is given, will overwrite mesh's ``volSizePx`` and set it globally at all nodes.
Args:
roi (pyfrp.subclasses.pyfrp_ROI.ROI): An ROI.
Keyword Args:
fnOut (str): Path to new .geo file.
segments (int): Number of segments used for convex hull of surface.
simplify (bool): Simplify surfaces of stl file.
iterations (int): Number of iterations used for simplification.
triangIterations (int): Number of iterations used for subdivision of surfaces.
addPoints (bool): Allow adding points inside surface triangles.
fixSurfaces (bool): Allow fixing of surfaces, making sure they are coherent with Gmsh requirements.
debug (bool): Print debugging messages.
volSizePx (float): Global mesh density.
volSizeLayer (float): Boundary layer mesh size.
thickness (float): Thickness of boundary layer.
cleanUp (bool): Clean up temporary files when finished.
approxBySpline (bool): Approximate curvatures by spline.
angleThresh (float): Threshold angle under which loops are summarized.
faces (list): List of faces.
onlyAbs (bool): Take absolute value of faces into account.
dim (int): Dimension of mesh.
Returns:
str: Path to new .geo file.
"""
if fnOut == None:
fnOut = self.simulation.embryo.geometry.fnGeo.replace(
".geo", "_" + roi.name + "_BL.geo")
#Build stl file for ROI
fnStl = roi.render2StlInGeometry(segments=segments,
fn=fnOut.replace(".geo", ".stl"))
#Read in stl file and simplify
dROI = pyfrp_gmsh_IO_module.readStlFile(fnStl)
if simplify:
dROI.simplifySurfaces(iterations=iterations,
triangIterations=triangIterations,
fixSurfaces=fixSurfaces,
debug=debug,
addPoints=bool(triangIterations > 0))
# If we extract faces, we have to put them in new ROI
if faces != 'all' and len(faces) > 0:
# Grab surfaces
sfs = dROI.getRuledSurfacesByNormal(faces, onlyAbs=onlyAbs)
# Insert in new domain
d2 = pyfrp_gmsh_geometry.domain()
for sf in sfs:
sf.extract(d=d2, debug=debug)
# Overwrite sfs and dROI
sfs = d2.ruledSurfaces
dROI = d2
#Approximate complicated curves by splines
if approxBySpline:
for sf in sfs:
sf.lineLoop.approxBySpline(angleThresh=angleThresh)
dROI.fixAllLoops()
#Read in geometry and merge
dGeo = self.simulation.embryo.geometry.readGeoFile()
dGeo.merge(dROI)
#Create boundary layer
blf = dGeo.addBoundaryLayerField(hfar=volSizeLayer,
hwall_n=volSizeLayer,
hwall_t=volSizeLayer,
thickness=thickness,
Quads=0.)
#Add surfaces to boundary layer mesh
blf.addFaceListByID(pyfrp_misc_module.objAttrToList(sfs, 'Id'))
blf.setAsBkgdField()
#Set global volSize
if volSizePx != None:
dGeo.setGlobalVolSize(volSizePx)
self.volSizePx = volSizePx
else:
dGeo.setGlobalVolSize(self.getVolSizePx())
#Write and set as new geometry
dGeo.writeToFile(fnOut)
self.simulation.embryo.geometry.setFnGeo(fnOut)
#Generate mesh
self.genMesh()
#Clean up temporary files
if cleanUp:
os.remove(fnStl)
os.remove(fnStl.replace(".stl", ".scad"))
return fnOut
def addBoundaryLayerAroundROI(self,roi,fnOut=None,segments=48,simplify=True,iterations=3,triangIterations=2,
fixSurfaces=True,debug=False,volSizePx=None,volSizeLayer=10,thickness=15.,cleanUp=True,
approxBySpline=True,angleThresh=0.95,faces='all',onlyAbs=True):
"""Adds boundary layer around ROI to the mesh.
Does this by:
* Generating a stl file describing ROI, see also :py:func:`pyfrp.subclasses.pyfrp_ROI.ROI.render2StlInGeometry`.
* Read in stl file as new :py:class:`pyfrp.modules.pyfrp_gmsh_geometry.domain` via
:py:func:`pyfrp.modules.pyfrp_gmsh_IO_module.readStlFile`.
* Simplify new geometry via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.simplifySurfaces`.
* Extracting selected surfaces via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.gmshElement.extract`.
* If selected, surface boundaries are approximated into splines via
:py:func:`pyfrp.modules.pyfrp_gmsh_geometry.gmshElement.extract`.
* Reading in geometry's .geo file via :py:func:`pyfrp.sublcasses.pyfrp_geometry.geometry.readGeoFile`.
* Merging ROI geometry into main geometry via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.merge`.
* Adding a boundary layer mesh via :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.addBoundaryLayerField`.
* Adding all surfaces of ROI's domain to boundary layer, see
:py:func:`pyfrp.modules.pyfrp_gmsh_geometry.boundaryLayerField.addFaceListByID`.
* Writing new .geo file.
* Setting new .geo file as ``fnGeo``.
* Running :py:func:`genMesh`.
* Clean up .stl and .scad files that are not needed anymore.
.. note:: ``volSizeLayer`` only allows a single definition of mesh size in layer. Note that the
:py:class:`pyfrp.modules.pyfrp_gmsh_geometry.boundaryLayerField` class allows different mesh sizes
normal and along surfaces. For more information, see its documentation.
.. note:: If no ``fnOut`` is given, will save a new .geo file in same folder as original ``fnGeo`` with subfix:
``fnGeo_roiName_BL.geo``.
.. note:: :py:func:`pyfrp.modules.pyfrp_gmsh_geometry.domain.simplifySurfaces` is not a simple procedure,
we recommend reading its documentation.
If ``volSizePx`` is given, will overwrite mesh's ``volSizePx`` and set it globally at all nodes.
Args:
roi (pyfrp.subclasses.pyfrp_ROI.ROI): An ROI.
Keyword Args:
fnOut (str): Path to new .geo file.
segments (int): Number of segments used for convex hull of surface.
simplify (bool): Simplify surfaces of stl file.
iterations (int): Number of iterations used for simplification.
triangIterations (int): Number of iterations used for subdivision of surfaces.
addPoints (bool): Allow adding points inside surface triangles.
fixSurfaces (bool): Allow fixing of surfaces, making sure they are coherent with Gmsh requirements.
debug (bool): Print debugging messages.
volSizePx (float): Global mesh density.
volSizeLayer (float): Boundary layer mesh size.
thickness (float): Thickness of boundary layer.
cleanUp (bool): Clean up temporary files when finished.
approxBySpline (bool): Approximate curvatures by spline.
angleThresh (float): Threshold angle under which loops are summarized.
faces (list): List of faces.
onlyAbs (bool): Take absolute value of faces into account.
dim (int): Dimension of mesh.
Returns:
str: Path to new .geo file.
"""
if fnOut==None:
fnOut=self.simulation.embryo.geometry.fnGeo.replace(".geo","_"+roi.name+"_BL.geo")
#Build stl file for ROI
fnStl=roi.render2StlInGeometry(segments=segments,fn=fnOut.replace(".geo",".stl"))
#Read in stl file and simplify
dROI=pyfrp_gmsh_IO_module.readStlFile(fnStl)
if simplify:
dROI.simplifySurfaces(iterations=iterations,triangIterations=triangIterations,fixSurfaces=fixSurfaces,debug=debug,addPoints=bool(triangIterations>0))
# If we extract faces, we have to put them in new ROI
if faces!='all' and len(faces)>0:
# Grab surfaces
sfs=dROI.getRuledSurfacesByNormal(faces,onlyAbs=onlyAbs)
# Insert in new domain
d2=pyfrp_gmsh_geometry.domain()
for sf in sfs:
sf.extract(d=d2,debug=debug)
# Overwrite sfs and dROI
sfs=d2.ruledSurfaces
dROI=d2
#Approximate complicated curves by splines
if approxBySpline:
for sf in sfs:
sf.lineLoop.approxBySpline(angleThresh=angleThresh)
dROI.fixAllLoops()
#Read in geometry and merge
dGeo=self.simulation.embryo.geometry.readGeoFile()
dGeo.merge(dROI)
#Create boundary layer
blf=dGeo.addBoundaryLayerField(hfar=volSizeLayer,hwall_n=volSizeLayer,hwall_t=volSizeLayer,thickness=thickness,Quads=0.)
#Add surfaces to boundary layer mesh
blf.addFaceListByID(pyfrp_misc_module.objAttrToList(sfs,'Id'))
blf.setAsBkgdField()
#Set global volSize
if volSizePx!=None:
dGeo.setGlobalVolSize(volSizePx)
self.volSizePx=volSizePx
else:
dGeo.setGlobalVolSize(self.getVolSizePx())
#Write and set as new geometry
dGeo.writeToFile(fnOut)
self.simulation.embryo.geometry.setFnGeo(fnOut)
#Generate mesh
self.genMesh()
#Clean up temporary files
if cleanUp:
os.remove(fnStl)
os.remove(fnStl.replace(".stl",".scad"))
return fnOut