From cdf085ae8a8a7c09e15ff51b9ff828d12dbbe778 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 25 Jan 2022 10:53:59 +0000
Subject: [PATCH] bugfix and add reporter
---
aliby/experiment.py | 2 +-
aliby/pipeline.py | 20 +++++++++++++++++++-
2 files changed, 20 insertions(+), 2 deletions(-)
diff --git a/aliby/experiment.py b/aliby/experiment.py
index 6dcc953d..d29c62fd 100644
--- a/aliby/experiment.py
+++ b/aliby/experiment.py
@@ -120,7 +120,7 @@ class MetaData:
)
def add_fields(self, fields_values: dict):
- for field, value in field_values.items():
+ for field, value in fields_values.items():
self.add_field(field, value)
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index b6dabd6c..bfe18173 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -29,6 +29,7 @@ from agora.io.signal import Signal
from extraction.core.extractor import Extractor, ExtractorParameters
from extraction.core.functions.defaults import exparams_from_meta
from postprocessor.core.processor import PostProcessor, PostProcessorParameters
+from postprocessor.compiler import ExperimentCompiler, PageOrganiser
logging.basicConfig(
filename="aliby.log",
@@ -82,7 +83,7 @@ class PipelineParameters(ParametersABC):
id=expt_id,
distributed=0,
tps=tps,
- directory=directory,
+ directory=str(directory),
strain="",
earlystop=dict(
min_tp=180,
@@ -130,6 +131,13 @@ class Pipeline(ProcessABC):
# for other processes
return cls(parameters=PipelineParameters.from_yaml(fpath))
+ @classmethod
+ def from_existing_h5(cls, fpath):
+ with h5py.File(fpath, "r") as f:
+ pipeline_parameters = PipelineParameters.from_yaml(f.attrs["parameters"])
+
+ return cls(pipeline_parameters)
+
def run(self):
# Config holds the general information, use in main
# Steps holds the description of tasks with their parameters
@@ -302,6 +310,7 @@ class Pipeline(ProcessABC):
self.parameters.postprocessing
).to_dict()
PostProcessor(filename, post_proc_params).run()
+
return True
except Exception as e: # bug in the trap getting
logging.exception(
@@ -317,6 +326,15 @@ class Pipeline(ProcessABC):
if session:
session.close()
+ try:
+ compiler = ExperimentCompiler(None, filepath)
+ tmp = compiler.run()
+ po = PageOrganiser(tmp, grid_spec=(3, 2))
+ po.plot()
+ po.save(fullpath / f"{directory}report.pdf")
+ except Exception as e:
+ print(e)
+
def check_earlystop(self, filename, es_parameters):
s = Signal(filename)
df = s["/extraction/general/None/area"]
--
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