app.reconstruct: Add 'force_use_grouped_pipeline' option

nabu/app/cli_configs.py

@@ -153,6 +153,11 @@ ReconstructConfig = {
         "default": -1,
         "type": int,
     },
+    "force_use_grouped_pipeline": {
+        "help": "Force nabu to use the 'grouped' reconstruction pipeline - slower but should work for all big datasets.",
+        "default": 0,
+        "type": int,
+    },
 }
 
 GenerateInfoConfig = {
@@ -267,4 +272,3 @@ DFFConfig = {
         "type": int,
     },
 }
-

nabu/app/reconstruct.py

@@ -115,6 +115,7 @@ def main():
     phase_method = None
     if "phase" in proc.processing_steps:
         phase_method = proc.processing_options["phase"]["method"]
+
     # Determine which pipeline should be used:
     #  - CTF filter needs to process full radios
     #  - Projections rotation can be chunked only for small angles
@@ -122,8 +123,11 @@ def main():
         reconstructor_cls = GroupedReconstructor
     if ("rotate_projections" in proc.processing_steps) and abs(proc.processing_options["rotate_projections"]["angle"]) > 15:
         reconstructor_cls = GroupedReconstructor
+    if bool(args["force_use_grouped_pipeline"]):
+        reconstructor_cls = GroupedReconstructor
     logger.debug("Using pipeline: %s" % reconstructor_cls.__name__)
 
+
     # Get extra options
     extra_options = {
         "gpu_mem_fraction": args["gpu_mem_fraction"],