From 206771937c1e402d9e07886945776a618b62ec29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 3 Aug 2021 10:58:04 +0100
Subject: [PATCH] clean ppparameters
Former-commit-id: 589ebd0fa6de82f9feed5ef84e3fc973fa888bc1
---
core/processor.py | 15 ++++++---------
examples/basic_processes.py | 10 +++++-----
2 files changed, 11 insertions(+), 14 deletions(-)
diff --git a/core/processor.py b/core/processor.py
index 90982209..87bc475f 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -15,19 +15,17 @@ class PostProcessorParameters(ParametersABC):
Anthology of parameters used for postprocessing
:merger:
:picker: parameters for picker
- :processes: List of processes that can be found in ./processes
- :datasets: Dictionary
+ :processes: Dict processes:[objectives], 'processes' are defined in ./processes/
+ while objectives are relative or absolute paths to datasets. If relative paths the
+ post-processed addresses are used.
#TODO Use cells to fetch updated cell indices
"""
- def __init__(
- self, merger=None, picker=None, processes=[], datasets=[], outpaths=[]
- ):
+ def __init__(self, merger=None, picker=None, processes=[]):
self.merger: MergerParameters = merger
self.picker: PickerParameters = picker
self.processes: List = processes
- self.outpaths = outpaths
self.datasets: Dict = datasets
@@ -43,7 +41,7 @@ class PostProcessorParameters(ParametersABC):
datasets={
"merger": "/extraction/general/None/area",
"picker": "/extraction/general/None/area",
- "processes": [],
+ "processes": {"dSignal": ["/general/None/area"]},
},
)
@@ -57,8 +55,7 @@ class PostProcessor:
self._signal = Signal(filename)
self._writer = Writer(filename)
- self.datasets = parameters["datasets"]
- self.outpaths = parameters["outpaths"]
+ # self.outpaths = parameters["outpaths"]
self.merger = Merger(parameters["merger"])
self.picker = Picker(
parameters=parameters["picker"], cells=Cells.from_source(filename)
diff --git a/examples/basic_processes.py b/examples/basic_processes.py
index b3bf6a24..c322fd4b 100644
--- a/examples/basic_processes.py
+++ b/examples/basic_processes.py
@@ -5,11 +5,11 @@ pp = PostProcessor(
"/shared_libs/pipeline-core/scripts/pH_calibration_dual_phl__ura8__by4741__01/ph_5_29_025store.h5",
params,
)
-# tmp = pp.run()
+tmp = pp.run()
import h5py
-f = h5py.File(
- "/shared_libs/pipeline-core/scripts/pH_calibration_dual_phl__ura8__by4741__01/ph_5_29_025store.h5",
- "a",
-)
+# f = h5py.File(
+# "/shared_libs/pipeline-core/scripts/pH_calibration_dual_phl__ura8__by4741__01/ph_5_29_025store.h5",
+# "a",
+# )
--
GitLab