def triToTst(triName, tstName):
'''reads a tri file, writes the tstfile'''
pdbD, triLineToNum, triPoints = readTri(triName)
#print pdbD, triLineToNum, triPoints
tstD = tstdata.tstDataWritable(False) # empty, now add stuff to it
tstD.dict['PDB_RECORD'] = pdbD.rawData # this one is easy
tstD.dict['POINT_XYZ'] = makePointXyz(triLineToNum)
tstD.dict['TRIANGLE_POINT'] = makeTriPoints(triPoints)
tstD.dict['TRIANGLE_NEIGHBOR'] = makeFakeTriNeighbors(
tstD.dict['TRIANGLE_POINT'])
tstD.dict['POINT_PDB_RECORD'] = nearbyPoints(tstD.dict['POINT_XYZ'], pdbD)
tstD.dict['TRIANGLE_PDB_RECORD'] = nearbyTriangles(
tstD.dict['POINT_PDB_RECORD'], tstD.dict['TRIANGLE_POINT'])
pointTriDict, triPointDict = makeDicts(tstD.dict['TRIANGLE_POINT'])
tstD.dict['POINT_TRIANGLE'], tstD.dict['POINT_NEIGHBOR'] = \
makePointTriAndNeighbor(pointTriDict, triPointDict)
tstD.dict['NORM_XYZ'] = calcNormals(
tstD.dict['POINT_XYZ'], triPointDict, pointTriDict)
tstD.dict['CURVATURE_XYZ'] = fakeForNow(tstD.dict['POINT_XYZ'])
tstD.dict['PROPERTY_XYZ'] = fakeForNow(tstD.dict['POINT_XYZ'])
#print tstD.dict.keys()
tstD.write(tstName)
def tstCavityRemoval(
tstFileName, tstFileNameOut, phiFileName=False, phiFileNameOut=False):
oldTst = tstdata.tstDataWritable(tstFileName) # read the file into the struct
allPoints, allTris, cavPoints, cavTris = findBiggestDisjointSets(
oldTst.dict['POINT_XYZ'], oldTst.dict['TRIANGLE_POINT'],
oldTst.dict['POINT_NEIGHBOR'])
#print len(allPoints), len(allTris), len(cavPoints), len(cavTris) #debug
#now remove everything that isn't allPoints and allTris
#first generate maps from old numbering to new numbering
mapPoints = makeMapLists(oldTst.dict['POINT_XYZ'], allPoints)
mapTris = makeMapLists(oldTst.dict['TRIANGLE_POINT'], allTris)
#ugh. phi map.
phiData = sharp_phi.phi(phiFileName) # read in the phimap if possible
gridD = grid.makeGridFromPhi(phiData, False)
#the False just makes it copy values
mins, maxs = phiData.getMinsMaxs()
maxVal = phiData.getMaxValues()
gridSize = 1.0/phiData.scale
#this function marks cavities as interior
cavTriTuples = geometry.cacheTriangle(
oldTst.dict['TRIANGLE_POINT'], oldTst.dict['POINT_XYZ'], cavTris)
#have to do this now before oldTst gets modified
orstHelper.decideInside(
gridD, cavTriTuples, cavPoints,
oldTst.dict['POINT_TRIANGLE'], oldTst.dict['POINT_XYZ'],
oldTst.dict['TRIANGLE_POINT'], maxVal)
#change anything inside cavities to max..
#now piece-by-piece fix each entry
newTN = replaceEntry(
oldTst.dict['TRIANGLE_NEIGHBOR'], mapTris, [mapTris, mapTris, mapTris])
oldTst.dict['TRIANGLE_NEIGHBOR'] = newTN
newPX = replaceEntry(
oldTst.dict['POINT_XYZ'], mapPoints, [False, False, False])
oldTst.dict['POINT_XYZ'] = newPX
newTP = replaceEntry(
oldTst.dict['TRIANGLE_POINT'], mapTris, [mapPoints, mapPoints, mapPoints])
oldTst.dict['TRIANGLE_POINT'] = newTP
newPT = replaceEntry(
oldTst.dict['POINT_TRIANGLE'], mapPoints, [False, mapTris],
extendToEnd=True)
oldTst.dict['POINT_TRIANGLE'] = newPT
newPN = replaceEntry(
oldTst.dict['POINT_NEIGHBOR'], mapPoints, [False, mapPoints],
extendToEnd=True)
oldTst.dict['POINT_NEIGHBOR'] = newPN
newNX = replaceEntry(
oldTst.dict['NORM_XYZ'], mapPoints, [False, False, False])
oldTst.dict['NORM_XYZ'] = newNX
newPPR = replaceEntry(oldTst.dict['POINT_PDB_RECORD'], mapPoints, [False])
oldTst.dict['POINT_PDB_RECORD'] = newPPR
newTPR = replaceEntry(oldTst.dict['TRIANGLE_PDB_RECORD'], mapTris, [False])
oldTst.dict['TRIANGLE_PDB_RECORD'] = newTPR
#don't touch PDB_RECORD...
newCX = replaceEntry(oldTst.dict['CURVATURE_XYZ'], mapPoints, [False])
oldTst.dict['CURVATURE_XYZ'] = newCX
newPX = replaceEntry(oldTst.dict['PROPERTY_XYZ'], mapPoints, [False])
oldTst.dict['PROPERTY_XYZ'] = newPX
#now write it back out...should probably tag it somehow....hmmm
oldTst.write(tstFileNameOut)
#write phi map
phiDataOut = sharp_phi.phi()
phiDataOut.createFromGrid(
gridD, gridSize, toplabel=phiData.toplabel,
head=phiData.head, title=phiData.title, botlabel=phiData.botlabel)
phiDataOut.write(phiFileNameOut)
