def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['start'] is None:
apDisplay.printError("a number of starting classes was not provided")
if self.params['end'] is None:
apDisplay.printError("a number of ending classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] is None:
self.params['numpart'] = npart
elif self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
self.boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.workingboxsize = math.floor(self.boxsize/self.params['bin'])
if not self.params['mask']:
self.params['mask'] = (self.boxsize/2)-2
self.workingmask = math.floor(self.params['mask']/self.params['bin'])
if self.params['mramethod'] == 'imagic':
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
def checkConflicts(self):
### check for IMAGIC installation
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
### check input parameters
if self.params['alignid'] is None:
apDisplay.printError("There is no stack ID specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run ID")
if self.params['MSAdistance'] is None:
apDisplay.printError("enter distance criteria for MSA program (i.e. eulidean, chisquare, modulation)")
return
def checkConflicts(self):
### check for IMAGIC installation
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
### check input parameters
if self.params['analysisId'] is None:
apDisplay.printError("There is no imagic analysis Id specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run ID")
if self.params['num_classes'] is None:
apDisplay.printError("enter number of classes that you want")
return
def checkConflicts(self):
### check for IMAGIC installation
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
### check input parameters
if self.params['analysisId'] is None:
apDisplay.printError("There is no imagic analysis Id specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run ID")
if self.params['num_classes'] is None:
apDisplay.printError("enter number of classes that you want")
return
def checkConflicts(self):
### check for IMAGIC installation
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
### run parameters
if self.params['templateStackId'] is None:
apDisplay.printError("enter template stack Id")
if self.params['stackId'] is None:
apDisplay.printError("enter a stack Id")
### references
if self.params['refs'] is True:
if self.params['thresh_refs'] is None or self.params['maskrad_refs'] is None:
apDisplay.printError("enter ALL parameters for preparing references")
### Multi Reference Alignment params
if self.params['mirror'] is None:
apDisplay.printError("enter option of using mirrors")
return
def checkConflicts(self):
### check for IMAGIC installation
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
### run parameters
if self.params['templateStackId'] is None:
apDisplay.printError("enter template stack Id")
if self.params['stackId'] is None:
apDisplay.printError("enter a stack Id")
### references
if self.params['refs'] is True:
if self.params['thresh_refs'] is None or self.params['maskrad_refs'] is None:
apDisplay.printError("enter ALL parameters for preparing references")
### Multi Reference Alignment params
if self.params['mirror'] is None:
apDisplay.printError("enter option of using mirrors")
return
def checkConflicts(self):
""" basic error handlign for running scripts """
### check for IMAGIC installation
try:
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
except:
c = "some IMAGIC functions, e.g. prealignment and angular reconstitution "
c+= "may not work. Use EMAN instead"
apDisplay.printWarning(c)
self.imagicroot = None
self.params['useEMAN1'] is True
### check class averages
if self.params['templatestackid'] is not None:
self.stackdata = appiondata.ApTemplateStackData.direct_query(self.params['templatestackid'])
self.clsname = self.stackdata['templatename']
self.params['apix'] = self.stackdata['apix']
self.params['boxsize'] = self.stackdata['boxsize']
self.params['oldavgs'] = os.path.join(self.stackdata['path']['path'], self.clsname[:-4]+".hed")
self.params['avgs'] = os.path.basename(self.clsname)
elif self.params['clusterid'] is not None:
self.stackdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
self.clsname = self.stackdata['avg_imagicfile']
self.params['apix'] = self.stackdata['clusterrun']['pixelsize']
self.params['boxsize'] = self.stackdata['clusterrun']['boxsize']
self.params['oldavgs'] = os.path.join(self.stackdata['path']['path'], self.clsname[:-4]+".hed")
self.params['avgs'] = self.clsname
elif self.params['classavgs'] is not None:
if self.params['apix'] is None:
apDisplay.printError("enter pixel size for manually uploaded classes")
self.params['oldavgs'] = self.params['classavgs']
bavgs = os.path.basename(self.params['classavgs'])
self.params['avgs'] = bavgs
else:
apDisplay.printError("enter class averages for the run")
if not os.path.isfile(os.path.abspath(self.params['oldavgs'])):
apDisplay.printError("cannot find input class averages")
if self.params['templatestackid'] is not None and self.params['clusterid'] is not None:
apDisplay.printError("enter either templatestack ID OR cluster ID")
if self.params['templatestackid'] is not None and self.params['classavgs'] is not None:
apDisplay.printError("enter either templatestack ID OR manually uploaded classes")
if self.params['clusterid'] is not None and self.params['classavgs'] is not None:
apDisplay.printError("enter either cluster ID OR manually uploaded classes")
### pretreatment
if self.imagicroot is not None and self.params['prealign'] is True:
warning = "particles will not be prealigned, IMAGIC is not installed or path "
warning+= "to IMAGIC cannot be located"
apDisplay.printWarning(warning)
### basic input parameters
self.params['numpart'] = apFile.numImagesInStack(self.params['oldavgs'])
if self.params['numpart'] < 3:
apDisplay.printError("need at least 3 class averages in stack to run")
self.params['boxsize'] = apFile.getBoxSize(self.params['oldavgs'])[0]
if self.params['num_volumes'] is None:
apDisplay.printError("specify the number of volumes to produce")
if self.params['apix'] is None:
apDisplay.printError("enter pixel size of class averages")
### refinement class averages
if self.params['r_templatestackid'] is not None:
self.rstackdata = appiondata.ApTemplateStackData.direct_query(self.params['r_templatestackid'])
self.rclsname = self.rstackdata['templatename']
self.params['refineapix'] = self.rstackdata['apix']
self.params['refineboxsize'] = self.rstackdata['boxsize']
self.params['oldravgs'] = os.path.join(self.rstackdata['path']['path'], self.rclsname[:-4]+".hed")
self.params['ravgs'] = os.path.basename(self.rclsname)
elif self.params['r_clusterid'] is not None:
self.rstackdata = appiondata.ApClusteringStackData.direct_query(self.params['r_clusterid'])
self.rclsname = self.rstackdata['avg_imagicfile']
self.params['refineapix'] = self.rstackdata['clusterrun']['pixelsize']
self.params['refineboxsize'] = self.rstackdata['clusterrun']['boxsize']
self.params['oldravgs'] = os.path.join(self.rstackdata['path']['path'], self.rclsname[:-4]+".hed")
self.params['ravgs'] = self.rclsname
elif self.params['refine_classavgs'] is not None:
rbavgs = os.path.basename(self.params['refine_classavgs'])
self.params['ravgs'] = rbavgs
self.params['refineboxsize'] = apFile.getBoxSize(self.params['oldravgs'])[0]
if self.params['refineapix'] is None:
warning = "refinement pixel size not specified ... assuming it is the same"
apDisplay.printWarning(warning)
self.params['refineapix'] = self.params['apix']
else:
# self.params['ravgs'] = None
self.params['oldravgs'] = self.params['avgs']
self.params['ravgs'] = self.params['avgs']
self.params['refineapix'] = self.params['apix']
self.params['refineboxsize'] = self.params['boxsize']
if not os.path.isfile(os.path.abspath(self.params['oldravgs'])):
warning = "cannot find class averages for refinement using the "
warning+= "specified path. Original averages will be used instead."
apDisplay.printWarning(warning)
self.params['oldravgs'] = self.params['avgs']
self.params['ravgs'] = self.params['avgs']
### check for scaling
if self.params['scale'] is True:
self.scalefactor = float(64.0 / self.params['boxsize'])
self.params['apix'] = self.params['apix'] / self.scalefactor
self.params['boxsize'] = 64
else:
self.scalefactor = 1
### angular reconstitution checks
if self.params['keep_ordered'] < 1.0: ### probably specified as a fraction
self.params['keep_ordered'] = self.params['keep_ordered'] * 100 ### convert to percentage
self.params['keep_ordered_num'] = self.params['numpart'] * self.params['keep_ordered'] / 100
### EMAN1 cross common lines checks
if self.params['useEMAN1'] is True:
if self.params['images_per_volume'] is None:
self.params['images_per_volume'] = int(self.params['numpart'] * 0.66)
if self.params['images_per_volume'] > self.params['numpart']:
warning = "number of images per volume greater than number of class averages "
warning+= "in input. Setting to (0.66)*(num_averages)"
apDisplay.printWarning(warning)
self.params['images_per_volume'] = int(self.params['numpart'] * 0.66)
if self.params['images_per_volume'] > self.params['numpart'] * 0.75:
warning = "consider asking for less images per volume to provide more variety "
warning = "during common lines search"
apDisplay.printWarning(warning)
### number of processors for threading ONLY works on a single node
self.params['threadnproc'] = apParam.getNumProcessors()
### refinement parameters
if self.params['linmask'] == 0:
self.params['linmask'] = (self.params['boxsize']-2)/2*self.params['apix']
if self.params['mask_radius'] is None and self.params['linmask'] != 0:
self.params['mask_radius'] = self.params['linmask'] * 1.2
elif self.params['mask_radius'] is None and self.params['linmask'] == 0:
self.params['mask_radius'] = self.params['boxsize'] * self.params['refineapix']
if self.params['outer_radius'] is None:
self.params['outer_radius'] = self.params['mask_radius'] * 0.8
return
