remove empty space between compartments

talent/layout_merge.py

@@ -3,6 +3,7 @@ import logging
 import numpy as np
 from itertools import combinations
 import sys
+import copy
 from typing import List, Any, Dict, Set, Tuple, Collection, NamedTuple
 
 
@@ -32,6 +33,8 @@ class CompartmentCCNode(NamedTuple):
             self.cmp_species[id].pos[0] += v[0]
             self.cmp_species[id].pos[1] += v[1]
 
+CompartmentGraphsIxs = Dict[str, List[int]]
+
 
 
 def merge_compartments(cmp_gs: Dict[str, List[nx.MultiGraph]], g_tgt: nx.MultiGraph) -> nx.MultiGraph:
@@ -275,7 +278,7 @@ def resolve_compartments_overlap(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], c
         shift = bb1.get_rb() * dir - bb2.get_lt() * dir #this is the "distance" (one componennt is 0) by which the bb2 needs to be shifted to resolve the overlap
 
         for ix in cmp_ixs2:
-            g_cc.nodes[ix]['data'].shift(shift)
+            get_cmp_cc_node(g_cc, ix).shift(shift)
 
         score = score_compartments_position(g_cc, gs, cmp_ixs1, cmp_ixs2)
         if score['cnt_intersections'] < min_score['cnt_intersections'] or (score['cnt_intersections'] == min_score['cnt_intersections'] and score['dist'] < min_score['dist']):
@@ -283,10 +286,10 @@ def resolve_compartments_overlap(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], c
             min_shift = shift
 
         for ix in cmp_ixs2:
-            g_cc.nodes[ix]['data'].shift(-shift)
+            get_cmp_cc_node(g_cc, ix).shift(-shift)
 
-    for ix in cmp_ixs2:
-        g_cc.nodes[ix]['data'].shift(min_shift)
+    # for ix in cmp_ixs2:
+    #     get_cmp_cc_node(g_cc, ix).shift(min_shift)
 
     #shift also the rest of the components which were in the direction of the shift
     for ix in range(len(gs)):
@@ -295,11 +298,11 @@ def resolve_compartments_overlap(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], c
             if ix in cmp_ixs2 or \
                     (min_shift[0] < 0 and bb.get_x1() < bb2.get_x2()) or (min_shift[0] > 0 and bb.get_x2() > bb2.get_x1()) or \
                     (min_shift[1] < 0 and bb.get_y1() < bb2.get_y2()) or (min_shift[1] > 0 and bb.get_y2() > bb2.get_y1()):
-                g_cc.nodes[ix]['data'].shift(min_shift)
+                get_cmp_cc_node(g_cc, ix).shift(min_shift)
                 lt.pan(gs[ix], min_shift)
 
 
-def get_compartment_dict(gs: List[nx.MultiGraph]) -> Dict[str, List[int]]:
+def get_compartment_dict(gs: List[nx.MultiGraph]) -> CompartmentGraphsIxs:
     cmp_ix: Dict[str, List[int]] = {}
     for i in range(len(gs)):
         cmp_name: str = gu.get_first_species(gs[i]).get_compartment_name()
@@ -311,11 +314,7 @@ def get_compartment_dict(gs: List[nx.MultiGraph]) -> Dict[str, List[int]]:
 
 
 
-def handle_overlaps(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], cmp_ix: Dict[str, List[int]]):
-
-
-    #First we group the connected components by compartment name
-
+def handle_overlaps(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], cmp_ix: CompartmentGraphsIxs):
 
     cmp_names = list(cmp_ix)
     for i in range(len(cmp_ix)):
@@ -323,15 +322,61 @@ def handle_overlaps(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], cmp_ix: Dict[s
         for j in range(i+1, len(cmp_ix)):
             cmp_name2 = cmp_names[j]
             #we are obtaining the bounding boxes here and not before the cycle because they change when the compartments overlaps are bing resolved
-            bb1: gr.Rectangle = gr.utils.get_bounding_box([g_cc.nodes[ix]['data'].bb for ix in cmp_ix[cmp_name1]])
-            bb2: gr.Rectangle = gr.utils.get_bounding_box([g_cc.nodes[ix]['data'].bb for ix in cmp_ix[cmp_name2]])
+            bb1: gr.Rectangle = gr.utils.get_bounding_box([get_cmp_cc_node(g_cc, ix).bb for ix in cmp_ix[cmp_name1]])
+            bb2: gr.Rectangle = gr.utils.get_bounding_box([get_cmp_cc_node(g_cc, ix).bb for ix in cmp_ix[cmp_name2]])
             if bb1.intersects_rectangle(bb2):
                 resolve_compartments_overlap(g_cc, gs, cmp_ix[cmp_name1], cmp_ix[cmp_name2], bb1, bb2)
 
-def clear_spaces(g_cc, gs):
-    NotImplemented
 
-def optimize_layout(g_cc, gs, cmp_ix):
+def get_cmp_cc_node(g: nx.MultiGraph, i: int) -> CompartmentCCNode:
+    return g.nodes[i]['data']
+
+
+def get_cmp_bbs(g_cc: nx.MultiGraph, cmp_ix: CompartmentGraphsIxs) -> Dict[str, gr.Rectangle]:
+    bbs = {}
+    for cmp_name in cmp_ix:
+        bbs[cmp_name] = gr.utils.get_bounding_box([get_cmp_cc_node(g_cc, ix).bb for ix in cmp_ix[cmp_name]])
+    return bbs
+
+
+
+
+def clear_spaces(g_cc: nx.MultiGraph, gs: List[nx.MultiGraph], cmp_ix: CompartmentGraphsIxs):
+
+    if len(cmp_ix) <= 1:
+        return
+
+    cmp_bb = get_cmp_bbs(g_cc, cmp_ix)
+
+    coords = []
+    for cmp_name, bb in cmp_bb.items():
+        coords.append({'coords': bb.get_lt(), 'begin': True, 'cmp_name': cmp_name})
+        coords.append({'coords': bb.get_rb(), 'begin': False, 'cmp_name': cmp_name})
+
+    sort_x = sorted(coords, key=lambda x: x['coords'][0])
+    sort_y = sorted(coords, key=lambda x: x['coords'][1])
+
+    for sort_coords, coord_ix in [(sort_x, 0), (sort_y, 1)]:
+        coord_i = sort_coords[1]
+        for i in range(2, len(sort_coords)):
+            # The first two coordinates are either one compartment or the beginning of two different compartments
+            coord_i_1 = coord_i
+            coord_i = sort_coords[i]
+            if not coord_i_1['begin'] and coord_i['begin']:
+                diff = coord_i['coords'][coord_ix] - coord_i_1['coords'][coord_ix]
+                shift = -(diff - settings.render.compartment_distance - settings.render.compartment_padding)
+                if shift < 0:
+                    shift_vect = np.array([0,0])
+                    shift_vect[coord_ix] = shift
+                    for j in range(i, len(sort_coords)):
+                        if sort_coords[j]['begin']:
+                            for ix in cmp_ix[sort_coords[j]['cmp_name']]:
+                                get_cmp_cc_node(g_cc, ix).shift(shift_vect)
+                                lt.pan(gs[ix], shift_vect)
+
+
+
+def optimize_layout(g_cc, gs):
     NotImplemented
 
 

talent/settings.py

@@ -11,6 +11,7 @@ class SettingsRender:
     compact_optimal_dist = 300
 
     compartment_padding = 80
+    compartment_distance = 10
 
     optimal_species_reaction_dist = 80
     optimal_neighboring_species_dist = 80