From 8bbeb63250a1faecfd0bfd8d3f5e33f30db83451 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 29 Mar 2022 11:40:08 +0100
Subject: [PATCH] bugfixes general parameters and post_pro legacy
---
aliby/pipeline.py | 26 ++++++++++++++++++++++++--
1 file changed, 24 insertions(+), 2 deletions(-)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index 1c35910c..a3bdec83 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -103,6 +103,16 @@ class PipelineParameters(ParametersABC):
),
)
}
+
+ for k, v in general.items(): # Overwrite general parameters
+ if k not in defaults["general"]:
+ defaults["general"][k] = v
+ elif isinstance(v, dict):
+ for k2, v2 in v.items():
+ defaults["general"][k][k2] = v2
+ else:
+ defaults["general"][k] = v
+
defaults["tiler"] = TilerParameters.default(**tiler).to_dict()
defaults["baby"] = BabyParameters.default(**extraction).to_dict()
defaults["extraction"] = exparams_from_meta(meta)
@@ -111,7 +121,7 @@ class PipelineParameters(ParametersABC):
).to_dict()
# for k in defaults.keys():
# exec("defaults[k].update(" + k + ")")
- # return cls(**{k: v for k, v in defaults.items()})
+ return cls(**{k: v for k, v in defaults.items()})
def load_logs(self):
parsed_flattened = parse_logfiles(self.log_dir)
@@ -180,6 +190,12 @@ class Pipeline(ProcessABC):
pipeline_parameters.general["directory"] = dir_path.parent
pipeline_parameters.general["filter"] = [fpath.stem for fpath in files]
+ # Fix legacy postprocessing parameters
+ post_process_params = pipeline_parameters.postprocessing.get("parameters", None)
+ if post_process_params:
+ pipeline_parameters.postprocessing["param_sets"] = copy(post_process_params)
+ del pipeline_parameters.postprocessing["parameters"]
+
return cls(pipeline_parameters)
@classmethod
@@ -196,6 +212,12 @@ class Pipeline(ProcessABC):
pipeline_parameters.general["directory"] = directory
pipeline_parameters.general["filter"] = Path(fpath).stem
+ # Fix legacy postprocessing parameters
+ post_process_params = pipeline_parameters.postprocessing.get("parameters", None)
+ if post_process_params:
+ pipeline_parameters.postprocessing["param_sets"] = copy(post_process_params)
+ del pipeline_parameters.postprocessing["parameters"]
+
return cls(pipeline_parameters, store=directory)
def run(self):
@@ -429,7 +451,7 @@ class Pipeline(ProcessABC):
)
tmp = copy(config["extraction"]["multichannel_ops"])
for op, (input_ch, op_id, red_ext) in tmp.items():
- if set(input_ch).difference(av_channels_wsub):
+ if not set(input_ch).issubset(av_channels_wsub):
del config["extraction"]["multichannel_ops"][op]
exparams = ExtractorParameters.from_dict(config["extraction"])
--
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