From c6bbb7fe7d4a02b47ffdc36d012aab7daa1e6961 Mon Sep 17 00:00:00 2001
From: unknown <david.hoksza@gmail.com>
Date: Tue, 22 Oct 2019 13:22:50 +0200
Subject: [PATCH] map transfer store split to map_transfer and store
---
talent/utils/transfer.py | 70 ++++++++++++++++++++++++----------------
1 file changed, 42 insertions(+), 28 deletions(-)
diff --git a/talent/utils/transfer.py b/talent/utils/transfer.py
index f40e98a..c6bb67d 100644
--- a/talent/utils/transfer.py
+++ b/talent/utils/transfer.py
@@ -8,6 +8,7 @@ import pickle
from sged import sged_graph as ed
from typing import List
+from typing import NamedTuple
import sys
sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../..")
@@ -23,6 +24,9 @@ from talent.beautification import BeautificationChain
from talent.beautification import BeautificationOp
from talent.beautification import BEAUTY_OPERATION_TYPE
+class MapTransferResult(NamedTuple):
+ bc: BeautificationChain
+ tmp: ReactionGraph
def get_rg_restricted_g(rg, g):
res = gu.deepcopy_graph(g)
@@ -72,7 +76,7 @@ def process_tgt(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, ddup):
return tgt_ccs
-def process_db(tmps_path, fmt, split_by_cmprtmnt, ddup, cc_before_ddup):
+def process_db(tmps_path, fmt, split_by_cmprtmnt, ddup, cc_before_ddup) -> List[ReactionGraph]:
"""
DB is a directory with json files of the compartments to be used as templates
:param dir_tmps:
@@ -244,14 +248,11 @@ def approximate_distances(tgt, tmps, node_edge_costs, cache_path):
return approx_res
-# def map_tgt_tmps(tgt_orig, tmps, use_cache, output_dir = ""):
-def map_transfer_store(tgt, tmps, cache_path, output_path, ix_connected_component) -> List[str]:
+def map_transfer(tgt, tmps, cache_path) -> List[MapTransferResult]:
- # tgt = tgt_orig.deepcopy()
+ assert (len(tmps) > 0)
- assert(len(tmps) > 0)
-
- output_fnames = []
+ rv: List[MapTransferResult] = []
ed_settings = settings.ed
@@ -260,23 +261,25 @@ def map_transfer_store(tgt, tmps, cache_path, output_path, ix_connected_componen
if len(tmps) > 1:
approx_res = approximate_distances(tgt, tmps, costs, cache_path)
- approx_res_ix_sort = sorted(range(len(approx_res)), key=lambda k: approx_res[k][0]['distance'] if len(approx_res[k]) > 0 else sys.float_info.max)
+ approx_res_ix_sort = sorted(range(len(approx_res)), key=lambda k: approx_res[k][0]['distance'] if len(
+ approx_res[k]) > 0 else sys.float_info.max)
else:
logging.info("Skipping approximation")
+
for i in range(min(settings.cnt_approx_to_try, len(tmps))):
if len(tmps) > 1:
- i_closest = approx_res_ix_sort[i]
+ ix_tmp = approx_res_ix_sort[i]
else:
- i_closest = 0
+ ix_tmp = 0
- tmp = tmps[i_closest]
+ tmp = tmps[ix_tmp]
logging.info("Picking {} as the template ({}. closest template)".format(tmp.get_name(), i))
- res = obtain_ed(tgt, tmp, costs[i_closest], cache_path, ed_settings)
+ res = obtain_ed(tgt, tmp, costs[ix_tmp], cache_path, ed_settings)
if len(res) == 0:
- res = approx_res[i_closest]
+ res = approx_res[ix_tmp]
logging.info("Used approximate mapping")
if len(res) == 0:
logging.info("No mapping available. Skipping...")
@@ -284,23 +287,33 @@ def map_transfer_store(tgt, tmps, cache_path, output_path, ix_connected_componen
logging.info("Used mapping: distance {} - {}".format(res[0]['distance'], res[0]['mapping']))
logging.info("Transferring layout from {} to {}".format(tmp.get_name(), tgt.get_name()))
- res = lt.transfer_layout(tgt, tmp, res[0]["mapping"]) #TODO result can contain multiple mappings with the same minimum distance
+ res = lt.transfer_layout(tgt, tmp, res[0][
+ "mapping"]) # TODO result can contain multiple mappings with the same minimum distance
bc = BeautificationChain(res)
- # bc.add([
- # # BeautificationStep(BEAUTY_OPERATION_TYPE.PUSH_AWAY_SIDE_SPECIES),
- # BeautificationOp(BEAUTY_OPERATION_TYPE.ALIGN_TO_GRID),
- # BeautificationOp(BEAUTY_OPERATION_TYPE.REMOVE_EMPTY_BANDS),
- # BeautificationOp(BEAUTY_OPERATION_TYPE.HANDLE_REACTION_SPECIES_OVERLAPS)
- # ])
- # bc.run()
+ rv.append(MapTransferResult(bc=bc, tmp=tmp))
+
+ return rv
+
+def map_transfer_store(tgt:ReactionGraph, tmps: List[ReactionGraph], cache_path: str, output_path: str) -> List[str]:
+
+ assert (len(tmps) > 0)
+
+ rv_fnames: List[str] = []
+
+ mtrs: List[MapTransferResult] = map_transfer(tgt, tmps, cache_path)
+
+ i = 0
+ for mtr in mtrs:
+ tmp = mtr.tmp
+ bc = mtr.bc
fname = "{}/{}-tmp_order_{}-tgt-ddup_{}_tmp-ddup_{}.pkl".format(output_path, get_tgt_tmp_name(tgt, tmp), i,
- tgt.is_ddup(), tmp.is_ddup())
- output_fnames.append(fname)
- # fname = "{}_cc-{}_k-{}.pkl".format(output_path, ix_connected_component, i)
+ tgt.is_ddup(), tmp.is_ddup())
+ i += 1
+ rv_fnames.append(fname)
logging.info("Storing transferred layout into {}".format(fname))
bc.save(fname)
- return output_fnames
+ return rv_fnames
def transfer(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, tmps_path, tmp_fmt,
@@ -331,14 +344,15 @@ def transfer(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, tmps_path, tmp_fmt
}
tgt_ccs = process_tgt(tgt_name, tgt_fname, tgt_fmt, split_by_cmprtmnt, ddup_tgt)
- tmps = process_db(tmps_path, tmp_fmt, split_by_cmprtmnt, ddup_tmp, tmp_cc_before_ddup)
+ tmps: List[ReactionGraph] = process_db(tmps_path, tmp_fmt, split_by_cmprtmnt, ddup_tmp, tmp_cc_before_ddup)
i = 0
for tgt in tgt_ccs:
logging.info("Mapping connected component {} (size {})".format(i, len(tgt.get_reaction_graph())))
i += 1
- fnames = map_transfer_store(tgt, tmps, cache_path, output_path, i)
- # TODO: remove in dist
+ # fnames = map_transfer_store(tgt, tmps, cache_path, output_path, i)
+ fnames = map_transfer_store(tgt, tmps, cache_path, output_path)
+ # TODO: remove in distribution
for fname in fnames:
export.export(input_path=fname, format="svg", minerva_instance=settings.minerva_instance, output_path=fname + ".svg")
export.export(input_path=fname, format="celldesigner", minerva_instance=settings.minerva_instance, output_path=fname + ".xml")
--
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