Python SpiderProtocol.__init__ Examples

Example #1

File: protocol_filters.py Project: azazellochg/scipion

 def __init__(self, **kwargs):
     ProtFilterParticles.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     self._op = "FQ"
     self._params = {'ext': 'stk', 
                     'particles': 'particles_filtered',
                     'particlesSel': 'particles_filtered_sel'}

Example #2

 def __init__(self, **kwargs):
     ProtCreateMask2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     
     self._params = {'ext': 'stk',
                     'inputImage': 'input_image',
                     'outputMask': 'output_mask'
                     }

Example #3

File: protocol_custommask.py Project: josegutab/scipion

 def __init__(self, **kwargs):
     ProtCreateMask2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     
     self._params = {'ext': 'stk',
                     'inputImage': 'input_image',
                     'outputMask': 'output_mask'
                     }

Example #4

 def __init__(self, **kwargs):
     ProtFilterParticles.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     self._op = "FQ"
     self._params = {
         'ext': 'stk',
         'particles': 'particles_filtered',
         'particlesSel': 'particles_filtered_sel'
     }

Example #5

File: protocol_custommask.py Project: I2PC/scipion

 def __init__(self, **kwargs):
     ProtCreateMask2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     # To avoid showing MPI box due to duplicated init
     self.allowMpi = False
     
     self._params = {'ext': 'stk',
                     'inputImage': 'input_image',
                     'outputMask': 'output_mask'
                     }

Example #6

File: protocol_custommask.py Project: yaizar/scipion-docker

    def __init__(self, **kwargs):
        ProtCreateMask2D.__init__(self, **kwargs)
        SpiderProtocol.__init__(self, **kwargs)
        # To avoid showing MPI box due to duplicated init
        self.allowMpi = False

        self._params = {
            'ext': 'stk',
            'inputImage': 'input_image',
            'outputMask': 'output_mask'
        }

Example #7

File: protocol_align_base.py Project: azazellochg/scipion

 def __init__(self, script, alignDir, **args):
     ProtAlign2D.__init__(self, **args)
     SpiderProtocol.__init__(self, **args)
     self._script = script
     self._alignDir = alignDir
     
     self._params = {'ext': 'stk',
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'average': join(self._alignDir, 'rfreeavg001'), # If change the name, change it in template batch
                     'particlesAligned': join(self._alignDir, 'stkaligned')
                     }  

Example #8

File: protocol_filters.py Project: yaizar/scipion-docker

    def __init__(self, **kwargs):
        ProtFilterParticles.__init__(self, **kwargs)
        SpiderProtocol.__init__(self, **kwargs)
        # To avoid showing MPI box due to duplicated init
        self.allowMpi = False

        self._op = "FQ"
        self._params = {
            'ext': 'stk',
            'particles': 'particles_filtered',
            'particlesSel': 'particles_filtered_sel'
        }

Example #9

File: protocol_classify_base.py Project: josegutab/scipion

 def __init__(self, script, classDir, **kwargs):
     ProtClassify2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     self._script = script
     self._classDir = classDir
     
     self._params = {'ext': 'stk',
                     '[class_dir]': self._classDir,
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'dendroPs': 'dendrogram',
                     'dendroDoc': '%s/docdendro' % self._classDir,
                     'averages': 'averages',                        
                     }  

Example #10

File: protocol_classify_base.py Project: EyeSeeTea/scipion-web

 def __init__(self, script, classDir, **kwargs):
     ProtClassify2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     self._script = script
     self._classDir = classDir
     
     self._params = {'ext': 'stk',
                     '[class_dir]': self._classDir,
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'dendroPs': 'dendrogram',
                     'dendroDoc': '%s/docdendro' % self._classDir,
                     'averages': 'averages'
                     }  

Example #11

File: protocol_align_base.py Project: I2PC/scipion

 def __init__(self, script, alignDir, **args):
     ProtAlign2D.__init__(self, **args)
     SpiderProtocol.__init__(self, **args)
     # To avoid showing MPI box due to duplicated init
     self.allowMpi = False
     self._script = script
     self._alignDir = alignDir
     
     self._params = {'ext': 'stk',
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'average': join(self._alignDir, 'rfreeavg001'), # If change the name, change it in template batch
                     'particlesAligned': join(self._alignDir, 'stkaligned')
                     }  

Example #12

File: protocol_align_base.py Project: EyeSeeTea/scipion-web

    def __init__(self, script, alignDir, **args):
        ProtAlign2D.__init__(self, **args)
        SpiderProtocol.__init__(self, **args)
        self._script = script
        self._alignDir = alignDir

        self._params = {
            'ext': 'stk',
            'particles': 'input_particles',
            'particlesSel': 'input_particles_sel',
            'average':
            join(self._alignDir, 'rfreeavg001'
                 ),  # If change the name, change it in template batch
            'particlesAligned': join(self._alignDir, 'stkaligned')
        }

Example #13

 def __init__(self, script, classDir, **kwargs):
     ProtClassify2D.__init__(self, **kwargs)
     SpiderProtocol.__init__(self, **kwargs)
     # To avoid showing MPI box due to duplicated init
     self.allowMpi = False
     self._script = script
     self._classDir = classDir
     
     self._params = {'ext': 'stk',
                     '[class_dir]': self._classDir,
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'dendroPs': 'dendrogram',
                     'dendroDoc': '%s/docdendro' % self._classDir,
                     'averages': 'averages'
                     }  

Example #14

    def __init__(self, script, alignDir, **args):
        ProtAlign2D.__init__(self, **args)
        SpiderProtocol.__init__(self, **args)
        # To avoid showing MPI box due to duplicated init
        self.allowMpi = False
        self._script = script
        self._alignDir = alignDir

        self._params = {
            'ext': 'stk',
            'particles': 'input_particles',
            'particlesSel': 'input_particles_sel',
            'average':
            join(self._alignDir, 'rfreeavg001'
                 ),  # If change the name, change it in template batch
            'particlesAligned': join(self._alignDir, 'stkaligned')
        }

Example #15

 def __init__(self, **kwargs):
     SpiderProtocol.__init__(self, **kwargs)
     self._caDir = 'CA'
     self._caPrefix = 'cas' 
     
     caFilePrefix = join(self._caDir, self._caPrefix + '_')
     
     self._params = {'ext': 'stk',
                     'particles': 'input_particles',
                     'particlesSel': 'input_particles_sel',
                     'outputParticles': 'output_particles',
                     'mask': 'mask',
                     # TO DO: read tags in case filenames change in SPIDER procedure
                     'imcFile': caFilePrefix + 'IMC',
                     'seqFile': caFilePrefix + 'SEQ',
                     'eigFile': caFilePrefix + 'EIG',
                     'eigenimages': join(self._caDir, 'stkeigenimg'),
                     'reconstituted': join(self._caDir, 'stkreconstituted')
                     }

Example #16

File: protocol_custommask.py Project: azazellochg/scipion

    def __init__(self, **kwargs):
        ProtCreateMask2D.__init__(self, **kwargs)
        SpiderProtocol.__init__(self, **kwargs)

        self._params = {"ext": "stk", "inputImage": "input_image", "outputMask": "output_mask"}