def preRun(self):
self.ImportProtocol()
self.Iteration_Working_Directory = os.path.join(self.pmprotWorkingDir,'Iter_00'+ str(self.iterationNo))
self.subtractionDir = self.workingDirPath(self.RunName)
self.volsDir = self.workingDirPath(self.volsDir)
self.referenceDir = self.workingDirPath(self.referenceDir)
self.subImgsDir = self.workingDirPath(self.subImgsDir)
self.scaledImages = self.workingDirPath(self.scaledImages)
self.resultsImagesName = self.workingDirPath(self.resultsImagesName)
self.localFilenameCurrentAngles = self.workingDirPath(self.localCurrentAngles)
self.CtfGroupDirectory = self.workingDirPath(self.CtfGroupDirectoryName)
tmpCTFname = join(self.CtfGroupDirectoryName,self.localStackCTFs)
self.projmatchStackCTFs = join(self.pmprotWorkingDir,tmpCTFname)
self.localStackCTFs = self.workingDirPath(tmpCTFname)
tmpCTFname = join(self.CtfGroupDirectoryName,self.localDocCTFs)
self.projmatchDocCTFs = join(self.pmprotWorkingDir,tmpCTFname)
self.localDocCTFs = self.workingDirPath(tmpCTFname)
if(self.MaxChangeInAngles > 100):
self.MaxChangeInAngles=-1
tmpFilename = self.current_angles
self.filename_currentAngles = os.path.join(self.Iteration_Working_Directory,tmpFilename)
if(self.doScaleImages):
md = MetaData(self.filename_currentAngles)
img = Image()
img.readApplyGeo(md, 1, False, DATA, ALL_IMAGES,False)
x=y=z=n=0
(x,y,z,n) = img.getDimensions()
factorX = x / self.dimX
if (self.dimY<0):
factorY = y / self.dimX
else:
factorY = y / self.dimY
self.dRradiusMax = round(self.dRradiusMax/factorX)
self.dRradiusMin = round(self.dRradiusMin/factorY)
fileList = []
for objId in md:
fileList.append(md.getValue(MDL_IMAGE, objId))
if len(fileList) > 10:
break
fn = getFilename()
if fn is None:
return
# if radius = -1 then we take half of the image dimension
if outerRadius < 0:
if fn.isImage():
img = Image()
#ROB: must convert to str first or PyString_AsString will complain
img.read(fn, HEADER)
xdim = img.getDimensions()[0]
outerRadius = xdim / 2
if unit == 'angstrom':
outerRadius *= sampling
gui.setVarValue(outerVarName, outerRadius)
from protlib_gui_ext import XmippBrowserMask
results = showBrowseDialog(parent=gui.master, browser=XmippBrowserMask, title="Select mask radius", allowFilter=False,
extra={'fileList': fileList, 'outerRadius': outerRadius,
'innerRadius': innerRadius, 'showInner': showInner,
'unit':unit, 'sampling':sampling})
if results:
# if (unit == 'angstrom'):
# results = [v*sampling for v in results]
gui.setVarValue(outerVarName, int(results[1]))
if showInner:
