analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
output="/Users/ludo/DEV/autoPACKresults/NM_Analysis_C2"
analyse.g.Resolution = 1.0
h.boundingBox=numpy.array(h.boundingBox)
fbox_bb=numpy.array(h.boundingBox)
# h.boundingBox[0]-=numpy.array([500.0,500.0,0.0])
# h.boundingBox[1]+=numpy.array([500.0,500.0,0.0])
d=analyse.doloop(1000,h.boundingBox,wrkDir,output,rdf=True,
render=False,twod=TWOD,use_file=True)#,fbox_bb=fbox_bb)
# if not NOGUI :
# afviewer.displayFill()
else :
gridfile = localdir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/grid_store"
h.placeMethod="RAPID"
h.saveResult = True
h.innerGridMethod = "bhtree"#jordan pure python ? sdf ?
# h.boundingBox = [[-250.0, -6500.0/2.0, -250.0], [250.0, 6500.0/2.0, 250.0]]
h.boundingBox =[[-2482, -2389.0, 100.0], [2495, 2466, 2181.0]]
# h.buildGrid(boundingBox=h.boundingBox,gridFileIn=None,rebuild=True ,
# gridFileOut=gridfile,previousFill=False)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,
gridFileOut=None,previousFill=False)
h.fill5(verbose = 0,usePP=True)
# if not NOGUI :
# afviewer.displayFill()
#analyse.grid_pack(h.boundingBox,wrkDir,seed=0, fill=1,vTestid = 0,vAnalysis = 1)#build grid and fill
#for i in range(2):
# print 'Collecting %d ...' % i
# n = gc.collect()
#h.loopThroughIngr(setJitter)
#raw_input()
if ANALYSIS:
# h.placeMethod="RAPID"
h.encapsulatingGrid=0
analyse = AnalyseAP(env=h, viewer=afviewer, result_file=None)
output=localdir+os.sep+"autoFillRecipeScripts/2DsphereFill/results/paper/"
analyse.g.Resolution = 1.0
d=analyse.doloop(100,h.boundingBox,wrkDir,output,rdf=True,render=False,twod=TWOD)
if not NOGUI :
afviewer.displayFill()
else :
gridfile = localdir+os.sep+"autoFillRecipeScripts/Mycoplasma/results/grid_store"
h.placeMethod="RAPID"
h.saveResult = True
h.innerGridMethod = "bhtree"#jordan pure python ? sdf ?
# h.boundingBox = [[-250.0, -6500.0/2.0, -250.0], [250.0, 6500.0/2.0, 250.0]]
h.boundingBox =[[-2482, -2389.0, 100.0], [2495, 2466, 2181.0]]
# h.buildGrid(boundingBox=h.boundingBox,gridFileIn=None,rebuild=True ,
# gridFileOut=gridfile,previousFill=False)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,
gridFileOut=None,previousFill=False)
h.fill5(verbose = 0,usePP=True)
# if not NOGUI :
# afviewer.displayFill()
#analyse.grid_pack(h.boundingBox,wrkDir,seed=0, fill=1,vTestid = 0,vAnalysis = 1)#build grid and fill
#for i in range(2):
# print 'Collecting %d ...' % i
# n = gc.collect()
fbox_bb = numpy.array(h.boundingBox)
# h.boundingBox[0]-=numpy.array([500.0,500.0,0.0])
# h.boundingBox[1]+=numpy.array([500.0,500.0,0.0])
d = analyse.doloop(5,
h.boundingBox,
wrkDir,
output,
rdf=True,
render=False,
twod=TWOD,
use_file=True) #,fbox_bb=fbox_bb)
# if not NOGUI :
# afviewer.displayFill()
else:
# h.saveResult = True
h.innerGridMethod = "floodfill"
h.buildGrid(boundingBox=h.boundingBox,
gridFileIn=None,
rebuild=True,
gridFileOut=None,
previousFill=False)
h.fill5(verbose=0, usePP=False)
if not NOGUI:
afviewer.displayFill()
#analyse.grid_pack(h.boundingBox,wrkDir,seed=0, fill=1,vTestid = 0,vAnalysis = 1)#build grid and fill
#for i in range(2):
# print 'Collecting %d ...' % i
# n = gc.collect()
# print 'Unreachable objects:', n
# print 'Remaining Garbage:',
analyse.g.Resolution = 1.0
h.boundingBox=numpy.array(h.boundingBox)
fbox_bb=numpy.array(h.boundingBox)
# h.boundingBox[0]-=numpy.array([500.0,500.0,0.0])
# h.boundingBox[1]+=numpy.array([500.0,500.0,0.0])
d=analyse.doloop(5,h.boundingBox,wrkDir,output,rdf=True,
render=False,twod=TWOD,use_file=True)#,fbox_bb=fbox_bb)
# if not NOGUI :
# afviewer.displayFill()
else :
autopack.testPeriodicity = False
gridfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\grid_store"
h.placeMethod="RAPID"
h.saveResult = True
resultfilename = h.resultfile = "D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_july"
h.innerGridMethod = "trimesh"
h.smallestProteinSize = 80.0
h.freePtsUpdateThrehod=0.0
#remove HUE,RIBO,DNAPOLY,PEPTIDE,RNA,DNA,Lipo
filterOutFiber(h)
h.loopThroughIngr(setJitter)
h.buildGrid(boundingBox=h.boundingBox,gridFileIn=gridfile,rebuild=True ,gridFileOut=gridfile,previousFill=False)
h.fill5(verbose = 0,usePP=usePP)
h.collectResultPerIngredient()
h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_1.json",useXref=False,mixed=True, kwds=["source","name"],result=True, transpose = True, grid=False,packing_options=False,indent=False,quaternion=True)
h.saveRecipe("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_H_2.json",useXref=False,mixed=True, kwds=["source","name"],result=True, transpose = False, grid=False,packing_options=False,indent=False,quaternion=True)
from autopack.IOutils import serializedRecipe, saveResultBinary, toBinary
djson, all_pos, all_rot = serializedRecipe(h,False,True,True,True)#transpose, use_quaternion, result=False, lefthand=False
with open("D:\\Data\\cellPACK_data\\Mycoplasma\\Mpn_Results_serialized.json","w") as f:
f.write(djson)