From 9432aaf28963d8ffc122fdf597f914939ce2afff Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Fri, 13 Jan 2023 11:48:58 +0000
Subject: [PATCH] final docs for postprocessor
---
src/agora/io/decorators.py | 8 ++++----
src/agora/io/signal.py | 19 +++++++++++++------
src/postprocessor/chainer.py | 1 +
src/postprocessor/grouper.py | 6 ++++--
4 files changed, 22 insertions(+), 12 deletions(-)
diff --git a/src/agora/io/decorators.py b/src/agora/io/decorators.py
index f0eea7e0..f4d8d023 100644
--- a/src/agora/io/decorators.py
+++ b/src/agora/io/decorators.py
@@ -1,6 +1,6 @@
#!/usr/bin/env jupyter
"""
-Convenience decorators that extend commonly-used methods or functions.
+Convenience decorators to extend commonly-used methods or functions.
"""
import typing as t
from functools import wraps
@@ -9,14 +9,14 @@ from functools import wraps
def _first_arg_str_to_df(
fn: t.Callable,
):
- """Ensures Signal-like classes convert strings to datasets when calling them"""
-
+ """Enable Signal-like classes to convert strings to data sets."""
@wraps(fn)
def format_input(*args, **kwargs):
cls = args[0]
data = args[1]
if isinstance(data, str):
+ # get data from h5 file
data = cls.get_raw(data)
+ # replace path in the undecorated function with data
return fn(cls, data, *args[2:], **kwargs)
-
return format_input
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 974fbfa5..165a7e03 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -42,7 +42,7 @@ class Signal(BridgeH5):
"Cy5",
"pHluorin405",
)
- # Alan: why "equivalences"?
+ # Alan: why "equivalences"? this variable is unused.
equivalences = {
"m5m": ("extraction/GFP/max/max5px", "extraction/GFP/max/median")
}
@@ -118,7 +118,13 @@ class Signal(BridgeH5):
@_first_arg_str_to_df
def retained(self, signal, cutoff=0.8):
- """Reduce a dataframe, or a list of dataframes, to a fraction of its former size, losing late time points."""
+ """
+ Load data (via decorator) and reduce the resulting dataframe.
+
+ Load data for a signal or a list of signals and reduce the resulting
+ dataframes to a fraction of their original size, losing late time
+ points.
+ """
if isinstance(signal, pd.DataFrame):
return self.get_retained(signal, cutoff)
elif isinstance(signal, list):
@@ -144,6 +150,7 @@ class Signal(BridgeH5):
tile_mo_da["trap"],
tile_mo_da["mother_label"],
tile_mo_da["daughter_label"],
+ a
)
).T
return lineage
@@ -161,7 +168,7 @@ class Signal(BridgeH5):
Parameters
----------
data : t.Union[str, pd.DataFrame]
- DataFrame or url to one.
+ DataFrame or path to one.
merges : t.Union[np.ndarray, bool]
(optional) 2-D array with three columns: the tile id, the mother label, and the daughter id.
If True, fetch merges from file.
@@ -215,7 +222,7 @@ class Signal(BridgeH5):
if not hasattr(self, "_available"):
self._available = []
with h5py.File(self.filename, "r") as f:
- f.visititems(self.store_signal_url)
+ f.visititems(self.store_signal_path)
for sig in self._available:
print(sig)
@@ -231,7 +238,7 @@ class Signal(BridgeH5):
if not hasattr(self, "_available"):
self._available = []
with h5py.File(self.filename, "r") as f:
- f.visititems(self.store_signal_url)
+ f.visititems(self.store_signal_path)
except Exception as e:
print("Error visiting h5: {}".format(e))
return self._available
@@ -344,7 +351,7 @@ class Signal(BridgeH5):
"""Get name of h5 file."""
return self.filename.stem
- def store_signal_url(
+ def store_signal_path(
self,
fullname: str,
node: t.Union[h5py.Dataset, h5py.Group],
diff --git a/src/postprocessor/chainer.py b/src/postprocessor/chainer.py
index ff3bce3e..a5387ccb 100644
--- a/src/postprocessor/chainer.py
+++ b/src/postprocessor/chainer.py
@@ -83,6 +83,7 @@ class Chainer(Signal):
**kwargs,
):
"""Load data from an h5 file."""
+ 1/0
if dataset in self.common_chains:
# get dataset for composite chains
data = self.common_chains[dataset](**kwargs)
diff --git a/src/postprocessor/grouper.py b/src/postprocessor/grouper.py
index edde1805..0bcfd841 100644
--- a/src/postprocessor/grouper.py
+++ b/src/postprocessor/grouper.py
@@ -91,7 +91,8 @@ class Grouper(ABC):
**kwargs,
):
"""
- Concatenate data for one signal from different h5 files, with one h5 file per position, into a dataframe.
+ Concatenate data for one signal from different h5 files, with
+ one h5 file per position, into a dataframe.
Parameters
----------
@@ -387,7 +388,7 @@ def concat_signal_ind(
**kwargs,
) -> pd.DataFrame:
"""
- Core function that retrieves an individual signal.
+ Retrieve an individual signal.
Applies filtering if requested and adjusts indices.
"""
@@ -482,6 +483,7 @@ class MultiGrouper:
return self._sigtable
# Alan: function seems out of place
+ # seaborn is not in pyproject.toml
def sigtable_plot(self) -> None:
"""
Plot number of chains for all available experiments.
--
GitLab