updated c code to work with new g++ compiler and updated optic_tract …

…seeds for Donald 60 and 150

bash/subtract_optic

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 # Subtracts the signal modelled by the corpus callosum from the fornix image
 
-REFERENCE_DIR="$HOME/fouts/params/image/reference"
+REFERENCE_DIR="$HOME/fouts/params/image/reference/"
 
 if [ $# -lt 1 ]; then
     echo "The directory to sort must be provided as an argument"

params/image/reference/donald/optic_tract.150.seed.txt

@@ -1,2 +1,2 @@
-23 19 0
--22 18 0
+19 47 0
+-14 43.5 2

params/image/reference/donald/optic_tract.60.seed.txt

@@ -1,2 +1,2 @@
-21 27.5 -8.5
--26 26.5 -8.5
+19 61 1
+-24.5 58.5 -4.5

python/hpc/invivo_sampling.py

@@ -14,7 +14,7 @@
 
 def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
                  prior_aux_freq, prior_density_low, prior_density_high, prior_hook, prior_thin,
-                 like_snr, init_name, samples_name, last_name):
+                 like_snr, init_name, samples_name, last_name, num_iterations):
     if args.like_noise_map:
         noise_option = '--like_noise_map {}'.format(os.path.join(work_dir, 'params', 'image',
                                                     'reference', args.like_noise_map))
@@ -38,7 +38,7 @@ def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
 time metropolis {dataset_path} {work_dir}/output/{init_name}.tct \
 {work_dir}/output/{samples_name}.tst {noise_option} \
 -exp_interp_extent {args.assumed_interp_extent} \
--walk_step_scale {args.step_scale} -num_iter {args.num_iterations} \
+-walk_step_scale {args.step_scale} -num_iter {num_iterations} \
 -sample_period {args.sample_period} -seed {random_seed} \
 -diff_encodings_location {work_dir}/params/diffusion/encoding_60.b \
 -prior_freq {prior_freq} {prior_aux_freq} \
@@ -59,7 +59,7 @@ def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
            samples_name=samples_name, last_name=last_name, random_seed=random_seed + 1,
            prior_freq=prior_freq, prior_aux_freq=prior_aux_freq, prior_density_low=prior_density_low,
            prior_density_high=prior_density_high, prior_hook=prior_hook, prior_thin=prior_thin,
-           noise_option=noise_option, last_sample=(args.num_iterations // args.sample_period) - 1)
+           noise_option=noise_option, last_sample=(args.num_iterations // args.sample_period) - 1, num_iterations=num_iterations)
     return cmd
 
 
@@ -76,6 +76,9 @@ def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
 parser.add_argument('--num_iterations', default=75000, type=int,
                     help="The number of interations in the metropolis sampling "
                          "(default: %(default)s)")
+parser.add_argument('--num_after_split_iterations', default=50000, type=int,
+                    help="The number of interations in the metropolis sampling after the split"
+                         "(default: %(default)s)")
 parser.add_argument('--sample_period', default=250, type=int,
                     help="The sample period of the metropolis sampling "
                           "(default: %(default)s)")
@@ -242,7 +245,8 @@ def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
                                  prior_density_high=prior_density_high, prior_hook=prior_hook,
                                  prior_thin=prior_thin, like_snr=like_snr, init_name='init',
                                  samples_name='samples_first' if args.split else 'samples',
-                                 last_name='end_first' if args.split else 'last')
+                                 last_name='end_first' if args.split else 'last',
+                                 num_iterations=args.num_iterations)
 
         if args.split:
 
@@ -260,7 +264,7 @@ def sampling_cmd(args, work_dir, dataset_path, random_seed, prior_freq,
                                      prior_density_high=prior_density_high, prior_hook=prior_hook,
                                      prior_thin=prior_thin, like_snr=like_snr,
                                      init_name='init_second', samples_name='samples',
-                                     last_name='last')
+                                     last_name='last', num_iterations=args.num_after_split_iterations)
 
             # Submit job to que
         hpc.submit_job(SCRIPT_NAME, cmd_line, args.np, work_dir, output_dir,

src/blossom5/MinCost/MinCost.cpp

@@ -222,17 +222,17 @@ void DualMinCost<CostType>::AddUnaryTerm(NodeId i, int objective_coef) {
 
 template<typename CostType>
 void DualMinCost<CostType>::SetLowerBound(NodeId i, CostType cmin) {
-    AddEdge(i, source, FLOW_INFTY, 0, -cmin);
+    this->AddEdge(i, source, FLOW_INFTY, 0, -cmin);
 }
 
 template<typename CostType>
 void DualMinCost<CostType>::SetUpperBound(NodeId i, CostType cmax) {
-    AddEdge(source, i, FLOW_INFTY, 0, cmax);
+    this->AddEdge(source, i, FLOW_INFTY, 0, cmax);
 }
 
 template<typename CostType>
 void DualMinCost<CostType>::AddConstraint(NodeId i, NodeId j, CostType cmax) {
-    AddEdge(i, j, FLOW_INFTY, 0, cmax);
+    this->AddEdge(i, j, FLOW_INFTY, 0, cmax);
 }
 
 template<typename CostType>

src/bts/fibre/base/set_reader.cpp.h

@@ -82,7 +82,7 @@ namespace BTS {
                             throw Exception(
                                     "No corresponding line found in extended properties file.");
 
-                        properties = parse_props_line(this->prop_hdr, line);
+                        properties = this->parse_props_line(this->prop_hdr, line);
 
                         set.extract_and_set_props(properties);
                         set.set_extend_props(properties);

src/bts/fibre/base/set_writer.cpp.h

@@ -76,7 +76,7 @@ namespace BTS {
 
                     set[elem_i].insert_props(properties_row);
 
-                    write_properties_row(this->elem_prop_hdr, properties_row, this->ext_elem_out);
+                    this->write_properties_row(this->elem_prop_hdr, properties_row, this->ext_elem_out);
 
                 }