From 821718e40651754a295e34e187ce81eb8fe536ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 13 Jul 2021 23:50:13 +0100
Subject: [PATCH] add template and peaks
Former-commit-id: 14e1d1850aa6d8f4d122eb65ff81749c48fd9e9c
---
core/processes/peaks.py | 44 ++++++++++++++++++++++++++++++++++++++
core/processes/savgol.py | 3 +--
core/processes/template.py | 29 +++++++++++++++++++++++++
3 files changed, 74 insertions(+), 2 deletions(-)
create mode 100644 core/processes/peaks.py
create mode 100644 core/processes/template.py
diff --git a/core/processes/peaks.py b/core/processes/peaks.py
new file mode 100644
index 00000000..15ddf950
--- /dev/null
+++ b/core/processes/peaks.py
@@ -0,0 +1,44 @@
+from scipy.signal import argrelmax, argrelmin
+from postprocessor.core.processes.base import ParametersABC, ProcessABC
+
+
+class PeaksParameters(ParametersABC):
+ """
+ Parameters
+ type : str {minima, maxima, "all"}. Determines which type of peaks to identify
+ order : int Parameter to pass to scipy.signal.argrelextrema indicating
+ how many points to use for comparison.
+ """
+
+ def __init__(self, type):
+ self.type = type
+
+ @classmethod
+ def default(cls):
+ return cls.from_dict({"type": "minima", "order": 3})
+
+
+class Peaks(ProcessABC):
+ """
+ Identifies a signal sharply dropping.
+ """
+
+ def __init__(self, parameters: PeaksParameters):
+ super().__init__(parameters)
+
+ def run(self, signal: pd.DataFrame):
+ """
+ Returns a boolean dataframe with the same shape as the
+ original signal but with peaks as true values.
+ """
+ peaks_mat = np.zeros_like(signal, dtype=bool)
+
+ comparator = np.less if self.parameters.type is "minima" else np.greater
+ peaks_ids = argrelextrema(new_df, comparator=comparator, order=order)
+ peaks_mat[peak_ids] = True
+
+ return pd.DataFrame(
+ peaks_mat,
+ index=signal.index,
+ columns=signal.columns,
+ )
diff --git a/core/processes/savgol.py b/core/processes/savgol.py
index 79fcdcaa..b006c422 100644
--- a/core/processes/savgol.py
+++ b/core/processes/savgol.py
@@ -25,7 +25,6 @@ class Savgol(ProcessABC):
"""
Apply Savitzky-Golay filter (works with NaNs, but it might return
NaN regions).
-
"""
def __init__(self, parameters: SavgolParameters):
@@ -38,7 +37,7 @@ class Savgol(ProcessABC):
return signal.apply(savgol_on_srs, 1)
@staticmethod
- def non_uniform_savgol(x, y, window, polynom):
+ def non_uniform_savgol(x, y, window: int, polynom: int):
"""
Applies a Savitzky-Golay filter to y with non-uniform spacing
as defined in x
diff --git a/core/processes/template.py b/core/processes/template.py
new file mode 100644
index 00000000..075f21b2
--- /dev/null
+++ b/core/processes/template.py
@@ -0,0 +1,29 @@
+from postprocessor.core.processes.base import ParametersABC, ProcessABC
+from postprocessor.core.functions.tracks import clean_tracks, merge_tracks, join_tracks
+
+
+class ParametersTemplate(ParametersABC):
+ """
+ Parameters
+ """
+
+ def __init__(
+ self,
+ ):
+ super().__init__()
+
+ @classmethod
+ def default(cls):
+ return cls.from_dict({})
+
+
+class ProcessTemplate(ProcessABC):
+ """
+ Template for process class.
+ """
+
+ def __init__(self, parameters: ParametersTemplate):
+ super().__init__(parameters)
+
+ def run(self):
+ pass
--
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