Source code for asap.pointmatch.create_tilepairs

#!/usr/bin/env python
import os

import renderapi

from asap.module.render_module import RenderModule
from asap.pointmatch.schemas import (
    TilePairClientParameters, TilePairClientOutputParameters)

if __name__ == "__main__" and __package__ is None:
    __package__ = "asap.pointmatch.create_tilepairs"


example = {
    "render": {
        "host": "http://em-131fs",
        "port": 8080,
        "owner": "gayathri",
        "project": "MM2",
        "client_scripts": "/allen/programs/celltypes/workgroups/em-connectomics/gayathrim/nc-em2/Janelia_Pipeline/render_20170613/render-ws-java-client/src/main/scripts"
    },
    "minZ": 1015,
    "maxZ": 1022,
    "zNeighborDistance": 0,
    "stack": "mm2_acquire_8bit_reimage",
    "xyNeighborFactor": 0.9,
    "excludeCornerNeighbors": "true",
    "excludeSameLayerNeighbors": "false",
    "excludeCompletelyObscuredTiles": "true",
    "output_dir":"/allen/programs/celltypes/workgroups/em-connectomics/gayathrim/nc-em2/Janelia_Pipeline/scratch/montageTilepairs"
}


class TilePairClientModule(RenderModule):
    default_schema = TilePairClientParameters
    default_output_schema = TilePairClientOutputParameters
    client_class = 'org.janelia.render.client.TilePairClient'
    client_script_name = 'run_ws_client.sh'

    def run(self):
        zvalues = self.render.run(
            renderapi.stack.get_z_values_for_stack, self.args['stack'])

        if self.args['minZ'] is not None:
            self.args['minZ'] = (
                self.args['minZ'] if self.args['minZ'] > min(zvalues)
                else min(zvalues))
        else:
            self.args['minZ'] = min(zvalues)

        if self.args['maxZ'] is not None:
            self.args['maxZ'] = (
                self.args['maxZ'] if self.args['maxZ'] < max(zvalues)
                else max(zvalues))
        else:
            self.args['maxZ'] = max(zvalues)

        tilepairJsonFile = "tile_pairs_%s_z_%d_to_%d_dist_%d.json" % (
            self.args['stack'], self.args['minZ'], self.args['maxZ'],
            self.args['zNeighborDistance'])
        tilepairJsonFile = os.path.join(
                                self.args['output_dir'],
                                tilepairJsonFile)

        tilepairs = self.render.run(
            renderapi.client.tilePairClient,
            self.args['stack'],
            self.args['minZ'],
            self.args['maxZ'],
            outjson=tilepairJsonFile,
            basestack=self.args['baseStack'],
            xyNeighborFactor=self.args['xyNeighborFactor'],
            zNeighborDistance=self.args['zNeighborDistance'],
            excludeCornerNeighbors=self.args['excludeCornerNeighbors'],
            excludeSameLayerNeighbors=self.args['excludeSameLayerNeighbors'],
            excludeCompletelyObscuredTiles=self.args[
                'excludeCompletelyObscuredTiles'])

        self.output({'tile_pair_file': tilepairJsonFile})


if __name__ == "__main__":
    module = TilePairClientModule()
    module.run()