add support for num_processes=0 in planning

nndet/planning/properties/instance.py

@@ -73,6 +73,10 @@ def run_analyze_instances(analyzer: DatasetAnalyzer,
         Dict: extract properties per case id [case_id, property_dict]
     """
     props_per_case = OrderedDict()
+    if analyzer.num_processes == 0:
+        props = [analyze_instances_per_case(*args) for args in zip(
+                 repeat(analyzer), analyzer.case_ids, repeat(all_classes))]
+    else:
         with Pool(analyzer.num_processes) as p:
             props = p.starmap(analyze_instances_per_case, zip(
                 repeat(analyzer), analyzer.case_ids, repeat(all_classes)))

nndet/planning/properties/intensity.py

@@ -80,16 +80,22 @@ def run_collect_intensity_properties(analyzer: DatasetAnalyzer,
             Evaluated statistics: `median`; `mean`; `std`; `min`; `max`; `percentile_99_5`; `percentile_00_5`
             `local_props`: contains a dict (with case ids) where statistics where computed per case
     """
-    with Pool(analyzer.num_processes) as p:
+    
     results = OrderedDict()
     for mod_id in range(num_modalities):
         logger.info(f"Processing intensity values of modality {mod_id}")
         results[mod_id] = OrderedDict()
 
+        if analyzer.num_processes == 0:
+            voxels = [get_voxels_in_foreground(*args) for args in
+                      zip(repeat(analyzer), analyzer.case_ids, repeat(mod_id))]
+            local_props = [compute_stats(v) for v in voxels]
+        else:
+            with Pool(analyzer.num_processes) as p:
                 voxels = p.starmap(get_voxels_in_foreground,
                                     zip(repeat(analyzer), analyzer.case_ids, repeat(mod_id)))
-
                 local_props = p.map(compute_stats, voxels)
+
         props_per_case = OrderedDict()
         for case_id, lp in zip(analyzer.case_ids, local_props):
             props_per_case[case_id] = lp

nndet/planning/properties/segmentation.py

@@ -117,6 +117,11 @@ def run_analyze_segmentation(
         Dict[Dict]: computed properties per case
     """
     props_per_case = OrderedDict()
+
+    if analyzer.num_processes == 0:
+        props = [analyze_fn(*args) for args in zip(
+            repeat(analyzer), analyzer.case_ids, repeat(all_classes))]
+    else:
         with Pool(analyzer.num_processes) as p:        
                 props = p.starmap(analyze_fn, zip(
                     repeat(analyzer), analyzer.case_ids, repeat(all_classes)))

scripts/preprocess.py

@@ -232,7 +232,7 @@ def run_check(data_dir: Path,
                  for case in cases_npz]
 
     if processes == 0:
-        result = [check_case(case_npz, case_pkl, remove=remove)
+        result = [check_case(case_npz, case_pkl, remove=remove, keys=keys)
                   for case_npz, case_pkl in zip(cases_npz, cases_pkl)]
     else:
         with Pool(processes=processes) as p: