Merge pull request #457 from dPys/development

Development

Dockerfile

@@ -86,7 +86,8 @@ RUN apt-get update -qq \
     && rm -r fsl* \
     && chmod 777 -R $FSLDIR/bin \
     && chmod 777 -R /usr/lib/fsl/5.0 \
-    && echo "tmpfs   /tmp         tmpfs   rw,nodev,nosuid,size=10G          0  0" >> /etc/fstab
+    && echo "tmpfs   /tmp         tmpfs   rw,nodev,nosuid,size=10G          0  0" >> /etc/fstab \
+    && echo "GRUB_CMDLINE_LINUX_DEFAULT="rootflags=uquota,pquota"" >> /etc/default/grub
 #    && wget --retry-connrefused --waitretry=5 --read-timeout=60 --timeout=60 -t 0 -q -O examples.tar.gz "https://osf.io/ye4vf/download" && tar -xvzf examples.tar.gz -C /tmp \
 #    && rm -rf examples.tar.gz
 

pynets/__about__.py

@@ -6,7 +6,7 @@
 # from ._version import get_versions
 # __version__ = get_versions()['version']
 # del get_versions
-__version__ = "1.0.3"
+__version__ = "1.0.4"
 
 __packagename__ = "pynets"
 __copyright__ = "Copyright 2016, Derek Pisner"

pynets/cli/pynets_run.py

@@ -3515,6 +3515,7 @@ def main():
             "PyNets not installed! Ensure that you are referencing the correct"
             " site-packages and using Python3.6+"
         )
+        sys.exit(1)
 
     if len(sys.argv) < 1:
         print("\nMissing command-line inputs! See help options with the -h"
@@ -3541,11 +3542,9 @@ def main():
         run_uuid = retval.get("run_uuid", None)
 
         retcode = retcode or int(pynets_wf is None)
-        if retcode != 0:
-            sys.exit(retcode)
+        if retcode == 1:
+            return retcode
 
-        # Clean up master process before running workflow, which may create
-        # forks
         gc.collect()
 
     mgr.shutdown()
@@ -3555,7 +3554,7 @@ def main():
 
         rmtree(work_dir, ignore_errors=True)
 
-    sys.exit(0)
+    return 0
 
 
 if __name__ == "__main__":

pynets/core/utils.py

@@ -1973,16 +1973,15 @@ def run(self):
             watchdog_thread.join()
         return 0
 
-    def _watchdog(self):
-        WATCHDOG_HARD_KILL_TIMEOUT = 7200
+    def _watchdog(self, watchdog_timeout=10800):
 
         self.last_progress_time = time.time()
 
         while self.last_progress_time == time.time():
             if self.shutdown.wait(timeout=5):
                 return
             last_progress_delay = time.time() - self.last_progress_time
-            if last_progress_delay < WATCHDOG_HARD_KILL_TIMEOUT:
+            if last_progress_delay < watchdog_timeout:
                 continue
             try:
                 signal.signal(signal.SIGQUIT, dumpstacks)

pynets/dmri/track.py

@@ -69,7 +69,7 @@ def reconstruction(conn_model, gtab, dwi_data, B0_mask):
             )
         except ValueError:
             import sys
-            sys.exit(0)
+            sys.exit(1)
 
     del dwi_data
 
@@ -191,7 +191,7 @@ def prep_tissues(
             raise ValueError("Tissue classifier cannot be none.")
         except ValueError:
             import sys
-            sys.exit(0)
+            sys.exit(1)
 
     del gm_data, wm_data, vent_csf_in_dwi_data
 
@@ -482,8 +482,7 @@ def track_ensemble(
         while float(stream_counter) < float(target_samples) and float(ix) < 0.50*float(len(all_combs)):
             with Parallel(n_jobs=nthreads, backend='loky',
                           mmap_mode='r+', temp_folder=joblib_dir,
-                          verbose=0, max_nbytes='50000M',
-                          timeout=timeout) as parallel:
+                          verbose=0, timeout=timeout) as parallel:
                 out_streams = parallel(
                     delayed(run_tracking)(
                         i, recon_path, n_seeds_per_iter, directget, maxcrossing,
@@ -502,14 +501,15 @@ def track_ensemble(
 
                 if len(out_streams) < min_streams:
                     ix += 2
-                    print(f"Fewer than {min_streams} streamlines tracked on last"
-                          f" iteration. Loosening tolerance and anatomical"
-                          f" constraints. Check {tissues4d} or {recon_path}"
-                          f" for errors...")
-                    if track_type != 'particle':
-                        tiss_class = 'wb'
-                    roi_neighborhood_tol = float(roi_neighborhood_tol) * 1.05
-                    min_length = float(min_length) * 0.95
+                    print(f"Fewer than {min_streams} streamlines tracked "
+                          f"on last iteration with cache directory: "
+                          f"{cache_dir}. Loosening tolerance and "
+                          f"anatomical constraints. Check {tissues4d} or "
+                          f"{recon_path} for errors...")
+                    # if track_type != 'particle':
+                    #     tiss_class = 'wb'
+                    roi_neighborhood_tol = float(roi_neighborhood_tol) * 1.25
+                    # min_length = float(min_length) * 0.9875
                     continue
                 else:
                     ix -= 1
@@ -531,19 +531,19 @@ def track_ensemble(
                 )
                 gc.collect()
                 print(Style.RESET_ALL)
-            os.system(f"rm -f {joblib_dir}/*")
+        os.system(f"rm -rf {joblib_dir}/*")
     except BaseException:
-        os.system(f"rm -f {tmp_files_dir} &")
+        os.system(f"rm -rf {tmp_files_dir} &")
         return None
 
     if ix >= 0.75*len(all_combs) and \
         float(stream_counter) < float(target_samples):
         print(f"Tractography failed. >{len(all_combs)} consecutive sampling "
               f"iterations with few streamlines.")
-        os.system(f"rm -f {tmp_files_dir} &")
+        os.system(f"rm -rf {tmp_files_dir} &")
         return None
     else:
-        os.system(f"rm -f {tmp_files_dir} &")
+        os.system(f"rm -rf {tmp_files_dir} &")
         print("Tracking Complete: ", str(time.time() - start))
 
     del parallel, all_combs
@@ -730,7 +730,7 @@ def run_tracking(step_curv_combinations, recon_path,
                 "ERROR: No valid tracking method(s) specified.")
         except ValueError:
             import sys
-            sys.exit(0)
+            sys.exit(1)
 
     # Filter resulting streamlines by those that stay entirely
     # inside the brain

pynets/runconfig.yaml

@@ -209,15 +209,15 @@ resource_dict: # Nipype workflow resource settings
       - 'get_fa_node':
         - (2, 1)
       - 'run_tracking_node':
-        - (3, 8)
+        - (3, 10)
       - 'thresh_diff_node':
         - (1, 1.5)
       - 'dsn_node':
         - (1, 2)
       - 'plot_all_node':
         - (1, 2)
       - 'streams2graph_node':
-        - (3, 4)
+        - (3, 6)
       - 'build_multigraphs_node':
         - (2, 8)
       - 'plot_all_struct_func_node':

pynets/stats/benchmarking.py

@@ -449,19 +449,19 @@ def benchmark_reproducibility(comb, modality, alg, par_dict, disc,
                                     with open(label_file, 'r+') as f:
                                         node_dict = json.load(f)
                                     indices = [i['index'] for i in
-                                                      node_dict.values()]
+                                                      node_dict]
                                     if indices == ixs:
                                         coords = [i['coord'] for i in
-                                                         node_dict.values()]
+                                                         node_dict]
 
                                         df_coords = pd.DataFrame(
                                             [str(tuple(x)) for x in
                                              coords]).T
                                         df_coords.columns = [f"rsn-{comb_tuple[0]}_res-{comb_tuple[-2]}_{i}" for i in ixs]
                                         labels = [
-                                            list(i['label'].values())[7] for i
+                                            list(i['label'])[7] for i
                                             in
-                                            node_dict.values()]
+                                            node_dict]
 
                                         df_labels = pd.DataFrame(
                                             labels).T
@@ -520,7 +520,6 @@ def benchmark_reproducibility(comb, modality, alg, par_dict, disc,
                 df_summary.at[0, f"{lp}_icc"] = np.nan
                 coord_in = np.nan
                 label_in = np.nan
-                del c_icc
 
             dict_sum[f"{lp}_coord"] = coord_in
             dict_sum[f"{lp}_label"] = label_in
@@ -593,11 +592,11 @@ def benchmark_reproducibility(comb, modality, alg, par_dict, disc,
 if __name__ == "__main__":
     __spec__ = "ModuleSpec(name='builtins', loader=<class '_" \
                "frozen_importlib.BuiltinImporter'>)"
-    base_dir = '/scratch/04171/dpisner/HNU/HNU_outs/triple'
-    #base_dir = '/scratch/04171/dpisner/HNU/HNU_outs/outputs_language'
+    #base_dir = '/scratch/04171/dpisner/HNU/HNU_outs/triple'
+    base_dir = '/scratch/04171/dpisner/HNU/HNU_outs/outputs_language'
     thr_type = "MST"
-    icc = False
-    disc = True
+    icc = True
+    disc = False
     int_consist = False
     target_modality = 'dwi'
 
@@ -606,8 +605,10 @@ def benchmark_reproducibility(comb, modality, alg, par_dict, disc,
     #embedding_types = ['OMNI']
     embedding_types = ['OMNI', 'ASE']
     modalities = ['func', 'dwi']
-    rsns = ['kmeans']
-    #rsns = ['language']
+    #rsns = ['kmeans', 'triple']
+    #rsns = ['triple']
+    #rsns = ['kmeans']
+    rsns = ['language']
     #template = 'CN200'
     template = 'MNI152_T1'
     mets = ["global_efficiency",
@@ -719,7 +720,7 @@ def tuple_insert(tup, pos, ele):
             cache_dir = tempfile.mkdtemp()
 
             with Parallel(
-                n_jobs=128, require="sharedmem", backend='threading',
+                n_jobs=-1, require="sharedmem", backend='threading',
                 verbose=10, max_nbytes='20000M',
                 temp_folder=cache_dir
             ) as parallel:
@@ -734,8 +735,8 @@ def tuple_insert(tup, pos, ele):
             # outs = []
             # for comb in grid:
             #     outs.append(benchmark_reproducibility(
-            #         comb, modality, alg, par_dict,
-            #         disc, final_missingness_summary,
+            #         comb, modality, alg, sub_dict_clean,
+            #         disc, final_missingness_summary, icc_tmps_dir,
             #     ))
             df_summary = pd.concat([i for i in outs if i is not None and not i.empty], axis=0)
             df_summary = df_summary.dropna(axis=0, how='all')