cluster.py 文件源码

def to_json(self, fname='cluster.json', k=5, criterion='maxclust'):
        """ Convert clustered neurons into json file that can be loaded into 
        CATMAID selection table.

        Parameters
        ----------
        fname :     str, optional
                    Filename to save selection to
        k :         {int, float}
        criterion : {'maxclust','distance'}, optional
                    If `maxclust`, `k` clusters will be formed. If `distance`, 
                    clusters will be created at threshold `k`.

        See Also
        --------
        :func:`pymaid.plot.plot3d` 
                    Function called to generate 3d plot                  
        """        

        cmap = self.get_colormap(k=k, criterion=criterion)

        # Convert to 0-255
        cmap = { n : [ int(v*255) for v in cmap[n] ] for n in cmap }  

        data = [ dict(skeleton_id=int(n),
                     color="#{:02x}{:02x}{:02x}".format( cmap[n][0],cmap[n][1],cmap[n][2] ),
                     opacity=1
                     ) for n in cmap ]

        with open(fname, 'w') as outfile:
            json.dump(data, outfile)

        module_logger.info('Selection saved as %s in %s' % (fname, os.getcwd()))    

        return