def readStarFile(prot, outputSetObject, fileType, starFile=None, invert=True, returnTable=False):
warningMsg = None
# # Star file can be provided by the user or not, depending on the protocol invoking this method
# if not starFile:
# starFile = prot.starFile.get()
#
# # If the star file is currently in the extra folder of another protocol execution, the paths
# # generated with method _getExtraPath() will become wrong, but it doesn't have to be located there
# if 'extra' in starFile:
# starPath = ''
# else:
# starPath = dirname(starFile) + '/'
tomoTable = Table()
tomoTable.read(starFile)
if fileType == RELION_SUBTOMO_STAR:
labels = RELION_TOMO_LABELS
_relionTomoStar2Subtomograms(prot,outputSetObject, tomoTable, invert)
else: # fileType == PYSEG_PICKING_STAR:
labels = PYSEG_PICKING_LABELS
_pysegStar2Coords3D(prot, outputSetObject, tomoTable, invert)
if not tomoTable.hasAllColumns(labels):
missingCols = [name for name in labels if name not in tomoTable.getColumnNames()]
warningMsg = 'Columns %s\nwere not found in the star file provided.\nThe corresponding numerical ' \
'values will be considered as 0.' \
% ' '.join(['*' + colName + '*' for colName in missingCols])
if returnTable:
return warningMsg, tomoTable
else:
return warningMsg
def getTomoSetFromStar(prot, starFile):
samplingRate = prot.pixelSize.get()
imgh = ImageHandler()
tomoTable = Table()
tomoTable.read(starFile)
tomoList = [row.get(TOMO_NAME, FILE_NOT_FOUND) for row in tomoTable]
prot.tomoList = List(tomoList)
tomoNamesUnique = list(set(tomoList))
# Create a Volume template object
tomo = Tomogram()
tomo.setSamplingRate(samplingRate)
for fileName in tomoNamesUnique:
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
tomo.setOrigin(origin) # read origin from form
for index in range(1, n + 1):
tomo.cleanObjId()
tomo.setLocation(index, fileName)
tomo.setAcquisition(TomoAcquisition(**prot.acquisitionParams))
prot.tomoSet.append(tomo)
def _getTomogramsFromStar(self):
"""Get the tomograms names to generate the output setOfTomograms and vesicles subtomogras ref tomograms"""
tomoFileList = []
tomoTable = Table()
tomoTable.read(self._starFile)
for row in tomoTable:
tomoFileList.append(row.get(TOMOGRAM))
return tomoFileList
def _findVesicleCenter(self, starFileInit, starFilePreseg1):
ih = ImageHandler()
outputTable = self._createTable()
# Read preseg (vesicles not centered) table
presegTable = Table()
presegTable.read(starFilePreseg1)
# Read initial data
initTable = Table()
initTable.read(starFileInit)
# Generate the star file with the vesicles centered for the second pre_seg execution
for row, rowp in zip(initTable, presegTable):
tomo = row.get(TOMOGRAM, NOT_FOUND)
vesicle = row.get(VESICLE, NOT_FOUND)
materialIndex = row.get(PYSEG_LABEL, NOT_FOUND)
# Get the upper left corner of the vesicle in the original tomogram: _psSegOffX #7 _psSegOffY #8 _psSegOffZ
# #9 from output star file of pre_tomos_seg.py that do not distinguish inner and outer densities
xdimCorner = rowp.get(PYSEG_OFFSET_X, 0)
ydimCorner = rowp.get(PYSEG_OFFSET_Y, 0)
zdimCorner = rowp.get(PYSEG_OFFSET_Z, 0)
# Get the box dimensions, be sure that the Dimensions format is Dimensions: 239 x 1 x 298 x 298
# ((N)Objects x (Z)Slices x (Y)Rows x (X)Columns)
x, y, z, _ = ih.getDimensions(rowp.get(MASK, NOT_FOUND))
# Add row to output table
outputTable.addRow(
tomo,
vesicle,
materialIndex,
vesicle,
xdimCorner + x / 2,
ydimCorner + y / 2,
zdimCorner + z / 2,
)
outputTable.write(self.getVesiclesCenteredStarFile())