Example #1
0
 def start(self):
     self.log.info("Writing DataSet: %s" % self.output)
     dataset = DataSet(self.output, mode="w", name="VectorApp-%s" % self.method)
     for i, (data, file) in enumerate(self.yield_transform(with_filenames=True)):
         dataset[i] = data
         dataset.set_trajfn(i, file)
     dataset.close()
Example #2
0
 def _yield_input(self, with_filenames=False):
     if self.source == "vector":
         for data in self.vectorapp.yield_transform(with_filenames):
             yield data
     else:
         dataset = DataSet(self.input)
         for key in dataset.keys():
             if with_filenames:
                 yield dataset[key], dataset.get_trajfn(key)
             else:
                 yield dataset[key]
         self.input_provenance = dataset.provenance
         dataset.close()
Example #3
0
    def start(self):
        if not os.path.exists(self.input):
            self.error('No such file or directory: %s' % self.input)

        if not tables.is_pytables_file(self.input):
            self.error('Unrecognized format')

        try:
            ds = DataSet(self.input, 'r')
            self.print_dataset(ds)
            ds.close()
        except UnrecognizedFormatError:
            handle = tables.open_file(self.input)
            self.print_model(handle)
            handle.close()
Example #4
0
 def _yield_input(self, with_filenames=False):
     if self.source == 'tICA':
         for data in self.ticaapp.yield_transform(with_filenames):
             yield data
     elif self.source == 'vector':
         for data in self.vector.yield_transform(with_filenames):
             yield data
     elif self.source == 'precomputed':
         dataset = DataSet(self.input)
         for key in dataset.keys():
             if with_filenames:
                 yield dataset[key], dataset.get_trajfn(key)
             else:
                 yield dataset[key]
         self.input_provenance = dataset.provenance
         dataset.close()
     else:
         raise RuntimeError(self.source)
Example #5
0
    def start(self):
        self.fit()

        if self.mode == 'fit':
            self.log.info('Saving fit KCenters model to `%s`' % self.output)
            with tables.open_file(self.output, 'w') as f:
                self.kcenters.to_pytables(f.root)

        elif self.mode in ['fit_predict', 'predict']:
            self.log.info('Writing DataSet: %s' % self.output)
            dataset = DataSet(self.output, mode='w', name='KCenters')
            if self.source == 'precomputed':
                dataset.provenance = self.input_provenance

            for i, (data, fn) in enumerate(self.yield_transform(with_filenames=True)):
                dataset[i] = data
                dataset.set_trajfn(i, fn)
            dataset.close()
        else:
            raise RuntimeError(self.mode)
Example #6
0
    def start(self):
        self.fit()

        if self.mode == "fit":
            self.log.info("Saving fit tICA model to `%s`" % self.output)
            with tables.open_file(self.output, "w") as f:
                self.tica.to_pytables(f.root)
            return

        if self.mode in ["fit_transform", "transform"]:
            self.log.info("Writing DataSet: %s" % self.output)
            dataset = DataSet(self.output, mode="w", name="TICAApp")
            if self.source == "precomputed":
                dataset.provenance = self.input_provenance

            for i, (data, fn) in enumerate(self.yield_transform(with_filenames=True)):
                dataset[i] = data
                dataset.set_trajfn(i, fn)
            dataset.close()
        else:
            raise RuntimeError()