def mergeClassesStep(self):
if self.doGrouping:
from cryomethods.functions import NumpyImgHandler
npIh = NumpyImgHandler()
makePath(self._getLevelPath(self._level))
listVol = self._getFinalMaps()
matrix = npIh.getAllNpList(listVol, 2)
labels = self._clusteringData(matrix)
clsChange = 0
prevStar = self._getFileName('rawFinalData')
pTable = Table()
origStar = self._getFileName('input_star', lev=1, rLev=1)
opticsTable = Table(fileName=origStar, tableName='optics')
print("OPTABLE: ", origStar, opticsTable.size())
for row in pTable.iterRows(prevStar, key="rlnClassNumber",
tableName='particles'):
clsPart = row.rlnClassNumber
newClass = labels[clsPart - 1] + 1
newRow = row._replace(rlnClassNumber=newClass)
if not newClass == clsChange:
if not clsChange == 0:
self.writeStar(fn, ouTable, opticsTable)
clsChange = newClass
fn = self._getFileName('input_star', lev=self._level,
rLev=newClass)
tableIn = Table(fileName=prevStar, tableName='particles')
cols = [str(c) for c in tableIn.getColumnNames()]
ouTable = Table(columns=cols, tableName='particles')
ouTable.addRow(*newRow)
print("mergeClassesStep ouTable.size: ", ouTable.size())
self.writeStar(fn, ouTable, opticsTable)
else:
prevData = self._getFileName('rawFinalData')
finalData = self._getFileName('finalData')
prevModel = self._getFileName('rawFinalModel')
finalModel = self._getFileName('finalModel')
copyFile(prevData, finalData)
copyFile(prevModel, finalModel)
def _getNumberOfBodies(self):
table = Table(fileName=self._getFileName('input'))
return int(table.size())
def _mergeDataStar(self, rLev, callback):
def _getMapId(rMap):
try:
return self._mapsDict[rMap]
except:
return None
iters = self._lastIter(rLev)
#metadata to save all particles that continues
outData = self._getFileName('outputData', lev=self._level)
#metadata to save all final particles
finalData = self._getFileName('rawFinalData')
imgStar = self._getFileName('data', iter=iters,
lev=self._level, rLev=rLev)
opTable = Table(filename=imgStar, tableName='optics')
tableIn = Table(fileName=imgStar, tableName='particles')
print("IMGSTAR: ", imgStar, "PARTS: ", tableIn.size())
cols = [str(c) for c in tableIn.getColumnNames()]
outTable = Table(columns=cols, tableName='particles')
finalTable = Table(columns=cols, tableName='particles')
if os.path.exists(outData):
print("Exists ", outData)
tmpTable = Table()
for row in tmpTable.iterRows(outData, tableName='particles'):
outTable.addRow(*row)
if os.path.exists(finalData):
print("Exists ", finalData)
tpTable = Table()
for row in tpTable.iterRows(finalData, tableName='particles'):
finalTable.addRow(*row)
pTable = Table()
for row in pTable.iterRows(imgStar, key="rlnClassNumber",
tableName='particles'):
clsPart = row.rlnClassNumber
rMap = callback(iters, rLev, clsPart)
mapId = _getMapId(rMap)
while mapId is None:
for clsPart in range(1, self.numberOfClasses.get()+1):
rMap = callback(iters, rLev, clsPart)
mapId = _getMapId(rMap)
if mapId is not None:
break
if self.stopDict[mapId]:
# if mapId != newMapId:
# if newMapId != '00.000':
# print(mdClass)
# mdClass.write(classMd)
# classMd = self._getFileName('mdataForClass', id=mapId)
# mdClass = self._getMetadata(classMd)
# newMapId = mapId
classId = self._clsIdDict[mapId]
newRow = row._replace(rlnClassNumber=classId)
finalTable.addRow(*newRow)
else:
classId = int(mapId.split('.')[1])
newRow = row._replace(rlnClassNumber=classId)
outTable.addRow(*newRow)
# if self.stopDict[mapId]:
# if mdClass.size() != 0:
# mdClass.write(classMd)
if finalTable.size() != 0:
print("finalTable.size: ", finalTable.size())
self.writeStar(finalData, finalTable)
if outTable.size() != 0:
print("outTable.size: ", outTable.size())
self.writeStar(outData, outTable, opTable)
def convertInputStep(self, resetDeps, copyAlignment):
import random
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
"""
if self._level == 0:
makePath(self._getRunPath(self._level, 1))
imgStar = self._getFileName('input_star', lev=self._level, rLev=0)
self._convertStar(copyAlignment, imgStar)
opticsTable = Table(fileName=imgStar, tableName='optics')
partsTable = Table(fileName=imgStar, tableName='particles')
self._convertVol(ImageHandler(), self.inputVolumes.get())
mdSize = partsTable.size()
for i in range(9, 1, -1):
makePath(self._getRunPath(self._level, i))
mStar = self._getFileName('input_star', lev=self._level, rLev=i)
size = 10000 * i if mdSize >= 100000 else int(mdSize * 0.1 * i)
print("partsTable: ", size, i, mdSize)
partsTable._rows = random.sample(partsTable._rows, k=size)
self.writeStar(mStar, partsTable, opticsTable)
elif self._level == 1:
imgStar = self._getFileName('input_star', lev=self._level, rLev=1)
makePath(self._getRunPath(self._level, 1))
self._convertStar(copyAlignment, imgStar)
# find a clever way to avoid volume conversion if its already done.
self._convertVol(ImageHandler(), self.inputVolumes.get())
else:
lastCls = None
prevStar = self._getFileName('outputData', lev=self._level - 1)
firstStarFn = self._getFileName('input_star', lev=1, rLev=1)
# mdData = md.MetaData(prevStar)
opTable = Table(fileName=firstStarFn, tableName='optics')
tableIn = Table(fileName=prevStar, tableName='particles')
cols = [str(c) for c in tableIn.getColumnNames()]
pTable = Table()
for row in pTable.iterRows(prevStar, key="rlnClassNumber",
tableName='particles'):
clsPart = row.rlnClassNumber
if clsPart != lastCls:
makePath(self._getRunPath(self._level, clsPart))
if lastCls is not None:
print("writing %s" % fn)
# mdInput.write(fn)
self.writeStar(fn, newPTable, opTable)
paths = self._getRunPath(self._level, clsPart)
makePath(paths)
print ("Path: %s and newRlev: %d" % (paths, clsPart))
lastCls = clsPart
newPTable = Table(columns=cols, tableName='particles')
fn = self._getFileName('input_star', lev=self._level,
rLev=clsPart)
# objId = mdInput.addObject()
newPTable.addRow(*row)
# row.writeToMd(mdInput, objId)
print("writing %s and ending the loop" % fn)
self.writeStar(fn, newPTable, opTable)
