From 5c298b49498cd86f4eaded6202a354a44179cace Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 15 Oct 2021 13:54:20 +0100
Subject: [PATCH] change names
Former-commit-id: 20564313baff9451f0f8f86dc5300f4cfd8ffb3b
---
core/processes/aggregate.py | 31 ++++++++++++++++++++-----------
core/processes/picker.py | 2 +-
core/processor.py | 14 ++++++--------
3 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/core/processes/aggregate.py b/core/processes/aggregate.py
index 2efff075..cfe8e8f0 100644
--- a/core/processes/aggregate.py
+++ b/core/processes/aggregate.py
@@ -12,13 +12,13 @@ class aggregateParameters(ParametersABC):
reduction: str to be passed to a dataframe for collapsing across columns
"""
- def __init__(self, reduction):
+ def __init__(self, reductions):
super().__init__()
- self.reduction = reduction
+ self.reductions = reductions
@classmethod
def default(cls):
- return cls.from_dict({"reduction": "mean"})
+ return cls.from_dict({"reductions": ["mean", "median", "max"]})
class aggregate(ProcessABC):
@@ -31,13 +31,14 @@ class aggregate(ProcessABC):
def run(self, signals):
names = np.array([signal.index.names for signal in signals])
- if not np.all(names == names[0]):
- "Not all indices are the same, selecting smallest set"
- index = signals[0].index
- for s in signals[0:]:
- index = index.intersection(s.index)
+ index = signals[0].index
+ for s in signals[0:]:
+ index = index.intersection(s.index)
- signals = [s.loc[index] for s in signals]
+ tmp_signals = [s.loc[index] for s in signals]
+ for i, s in enumerate(signals):
+ tmp_signals[i].name = s.name
+ signals = tmp_signals
assert len(signals), "Signals is empty"
@@ -54,9 +55,17 @@ class aggregate(ProcessABC):
for ind in item.split("/")
if ind not in bad_words
]
- colnames = ["_".join(get_keywords(s)) for s in signals]
+ colnames = [
+ "_".join(get_keywords(s) + [red])
+ for s in signals
+ for red in self.parameters.reductions
+ ]
concat = pd.concat(
- [getattr(signal, self.parameters.reduction)(axis=1) for signal in signals],
+ [
+ getattr(signal, red)(axis=1)
+ for signal in signals
+ for red in self.parameters.reductions
+ ],
names=signals[0].index.names,
axis=1,
)
diff --git a/core/processes/picker.py b/core/processes/picker.py
index 23be1f70..a7221e6f 100644
--- a/core/processes/picker.py
+++ b/core/processes/picker.py
@@ -10,7 +10,7 @@ from utils_find_1st import find_1st, cmp_equal
import numpy as np
import pandas as pd
-from core.cells import CellsHDF
+from pcore.cells import CellsHDF
from agora.base import ParametersABC, ProcessABC
from postprocessor.core.functions.tracks import max_ntps, max_nonstop_ntps
diff --git a/core/processor.py b/core/processor.py
index 9e6130f6..81c54b6f 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -8,10 +8,10 @@ import pandas as pd
from tqdm import tqdm
from agora.base import ParametersABC
-from core.io.writer import Writer
-from core.io.signal import Signal
+from pcore.io.writer import Writer
+from pcore.io.signal import Signal
-from core.cells import Cells
+from pcore.cells import Cells
from postprocessor.core.processes.merger import mergerParameters, merger
from postprocessor.core.processes.picker import pickerParameters, picker
@@ -82,15 +82,13 @@ class PostProcessorParameters(ParametersABC):
"/extraction/em_ratio_bgsub/np_max/median",
"/extraction/gsum/np_max/median",
"/extraction/gsum/np_max/mean",
- "/postprocessing/bud_metric/extraction_general_None_volume",
- "/postprocessing/bud_metric/extraction_em_ratio_np_max_mean",
- "/postprocessing/bud_metric/extraction_em_ratio_np_max_median",
+ "postprocessing/bud_metric/extraction_general_None_volume",
+ "postprocessing/bud_metric/extraction_em_ratio_np_max_mean",
+ "postprocessing/bud_metric/extraction_em_ratio_np_max_median",
"postprocessing/dsignal/extraction_general_None_volume",
"postprocessing/dsignal/postprocessing_bud_metric_extraction_general_None_volume",
"postprocessing/dsignal/postprocessing_bud_metric_extraction_em_ratio_np_max_median",
"postprocessing/dsignal/postprocessing_bud_metric_extraction_em_ratio_np_max_mean",
- "postprocessing/dsignal/postprocessing_bud_metric_extraction_em_ratio_bgsub_np_max_median",
- "postprocessing/dsignal/postprocessing_bud_metric_extraction_em_ratio_bgsub_np_max_mean",
]
],
),
--
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