Merge pull request #23 from Social-Evolution-and-Behavior/debug-jana

Fixes for issues #17 and #20, and a few more minor issues

antrax/cli.py

@@ -268,9 +268,13 @@ def solve(explist, *, glist: parse_movlist=None, movlist: parse_movlist=None, cl
         for e in explist:
 
             eglist = glist if glist is not None else e.glist
+
             emlist = [e.ggroups[g - 1] for g in eglist]
             emlist = [m for grp in emlist for m in grp]
 
+            if movlist is not None:
+                emlist = [m for m in emlist if m in movlist]
+
             hpc_options['dry'] = dry
             hpc_options['classifier'] = classifier
             hpc_options['missing'] = missing
@@ -282,19 +286,25 @@ def solve(explist, *, glist: parse_movlist=None, movlist: parse_movlist=None, cl
                 for c in eclist:
                     hpc_options['c'] = c
                     hpc_options['waitfor'] = None
+                    if step == 0 or step == 1:
+                        jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=1)
+                        hpc_options['waitfor'] = jid
+                    if step == 0 or step == 2:
+                        jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=2)
+                        hpc_options['waitfor'] = jid
+                    if step == 0 or step == 3:
+                        jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=3)
+            else:
+                hpc_options['c'] = None
+                hpc_options['waitfor'] = None
+                if step == 0 or step == 1:
                     jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=1)
                     hpc_options['waitfor'] = jid
+                if step == 0 or step == 2:
                     jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=2)
                     hpc_options['waitfor'] = jid
+                if step == 0 or step == 3:
                     jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=3)
-            else:
-                hpc_options['c'] = None
-                hpc_options['waitfor'] = None
-                jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=1)
-                hpc_options['waitfor'] = jid
-                jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=2)
-                hpc_options['waitfor'] = jid
-                jid = antrax_hpc_job(e, 'solve', opts=hpc_options, solve_step=3)
 
     else:
 

antrax/hpc.py

@@ -259,6 +259,7 @@ def antrax_hpc_job(ex, step, opts, solve_step=None):
         print('Job number ' + str(jid) + ' was submitted')
         print('')
     else:
+        jid = 0
         print('Dry run, no job submitted.')
         print('')
 

matlab/@tracklet/tracklet.m

@@ -741,8 +741,19 @@ function load_ids(trjs)
                 if ~isfile(f)
                     continue
                 end
+
                 T = readtable(f);
 
+                % patch to a weird case when sometimes matlab doesnt
+                % understand the csv structure (GitHub issue #20)
+                if ~ismember('tracklet', T.Properties.VariableNames)
+                    T = readtable(f,'Delimiter',',');
+                end
+
+                if isempty(T)
+                    return
+                end
+
                 ix = ismember(T.tracklet,mtrjnames);
                 T = T(ix,:);
 

matlab/@trgraph/solve.m

@@ -519,7 +519,15 @@ function eliminate_cc(G,cc,id)
     for i=1:length(assigned_nodes)
         idix = find(G.assigned_ids(assigned_nodes(i),:));
         for j=1:length(idix)
-            score = G.assignment_scores(assigned_nodes(i),idix(j));
+            %try
+                score = G.assignment_scores(assigned_nodes(i),idix(j));
+            %catch ME
+            %    report('E','error in propagate_all')
+            %    report('I',['node is ',num2str(assigned_nodes(i))])
+            %    report('I',['size of assignment scores is ',num2str(size(G.assignment_scores))])
+            %    report('I',['size of assignment ids is ',num2str(size(G.assigned_ids))])
+            %    rethrow(ME)
+            %end
             nij = propagate(G,assigned_nodes(i),idix(j),score);
             n = n + nij;
         end
@@ -533,6 +541,8 @@ function eliminate_cc(G,cc,id)
 nnp=nn;
 
 report('I','Biconnected components condition (positive)')
+
+if ~isempty(G.pairs)
 G.pairs = G.pairs(argsort(G.pairs(:,3)),:);
 while true
     n=0;
@@ -569,6 +579,7 @@ function eliminate_cc(G,cc,id)
         break
     end
 end
+end
 
 if nn==nnp
     return

matlab/@trgraph/trgraph.m

@@ -484,6 +484,7 @@ function filter_impossible_jumps(G)
             report('I','done distance mat');
             sset = find(din>1 & ~ignore);
 
+            pairs = {};
 
             for six=1:length(sset)%,G.NumWorkers)
 
@@ -528,7 +529,9 @@ function filter_impossible_jumps(G)
                 named_pairs(i).dist = pairs(i,3);
             end
 
-            pairs = pairs(argsort(pairs(:,3)),:);
+            if ~isempty(pairs)
+                pairs = pairs(argsort(pairs(:,3)),:);
+            end
 
             G.pairs = pairs;
 
@@ -744,6 +747,7 @@ function set_data(G)
                 if ~isempty(G.assigned_ids)
                     GS(i).assigned_ids = G.assigned_ids(ix,:);
                     GS(i).possible_ids = G.possible_ids(ix,:);
+                    GS(i).assignment_scores = G.assignment_scores(ix,:);
                     GS(i).finalized = G.finalized(ix,:);
                 end
                 GS(i).isopen = false;