From 6f21c34889776cc19342649a07ca8fc1667b4583 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 16 Jun 2021 18:34:31 +0100
Subject: [PATCH] add base and signal
Former-commit-id: 828ea0f0c3348532c794417d6714d279576a3291
---
core/io/base.py | 9 +++++++++
core/io/signal.py | 35 +++++++++++++++++++++++++++++++++++
2 files changed, 44 insertions(+)
create mode 100644 core/io/base.py
create mode 100644 core/io/signal.py
diff --git a/core/io/base.py b/core/io/base.py
new file mode 100644
index 00000000..a757a96e
--- /dev/null
+++ b/core/io/base.py
@@ -0,0 +1,9 @@
+import h5py
+
+
+class BridgeH5:
+ def __init__(self, file):
+ self._hdf = h5py.File(file, "r")
+
+ def close(self):
+ self._hdf.close()
diff --git a/core/io/signal.py b/core/io/signal.py
new file mode 100644
index 00000000..5f3e8c6d
--- /dev/null
+++ b/core/io/signal.py
@@ -0,0 +1,35 @@
+from postprocessor.core.io.base import BridgeH5
+
+
+class Signal(BridgeH5):
+ """
+ Class that fetches data from the hdf5 storage for post-processing
+ """
+
+ def __init__(self, file):
+ super().__init__(file)
+
+ def __getitem__(self, dataset):
+ dset = self._hdf[dataset][()]
+ attrs = self._hdf[dataset].attrs
+ first_dataset = "/" + dataset.split("/")[0] + "/"
+ timepoints = self._hdf[first_dataset].attrs["processed_timepoints"]
+
+ if "cell_label" in self._hdf[dataset].attrs:
+ ids = pd.MultiIndex.from_tuples(
+ zip(attrs["trap"], attrs["cell_label"]), names=["trap", "cell_label"]
+ )
+ else:
+ ids = pd.Index(attrs["trap"], names=["trap"])
+
+ return pd.DataFrame(dset, index=ids, columns=timepoints)
+
+ @staticmethod
+ def _if_ext_or_post(name):
+ if name.startswith("extraction") or name.startswith("postprocessing"):
+ if len(name.split("/")) > 3:
+ return name
+
+ @property
+ def datasets(self):
+ return signals._hdf.visit(self._if_ext_or_post)
--
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