From 0f3748152a7100ad472c1e7c6a899bf21ded1992 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Thu, 13 Jan 2022 18:13:28 +0000
Subject: [PATCH] rm group and update deps
---
aliby/grouper.py | 175 -----------------------------------------------
poetry.lock | 20 +++---
pyproject.toml | 10 +--
3 files changed, 17 insertions(+), 188 deletions(-)
delete mode 100644 aliby/grouper.py
diff --git a/aliby/grouper.py b/aliby/grouper.py
deleted file mode 100644
index 33180641..00000000
--- a/aliby/grouper.py
+++ /dev/null
@@ -1,175 +0,0 @@
-#!/usr/bin/env python3
-
-from abc import ABC, abstractmethod, abstractproperty
-from pathlib import Path
-from pathos.multiprocessing import Pool
-
-import h5py
-import numpy as np
-import pandas as pd
-
-from agora.io.signal import Signal
-
-
-class Grouper(ABC):
- """
- Base grouper class
- """
-
- files = []
-
- def __init__(self, dir):
- self.files = list(Path(dir).glob("*.h5"))
- self.load_signals()
-
- def load_signals(self):
- self.signals = {f.name[:-3]: Signal(f) for f in self.files}
-
- @property
- def fsignal(self):
- return list(self.signals.values())[0]
-
- @property
- def siglist(self):
- return self.fsignal.datasets
-
- @abstractproperty
- def group_names():
- pass
-
- def concat_signal(self, path, reduce_cols=None, axis=0, pool=8):
- group_names = self.group_names
- sitems = self.signals.items()
- if pool:
- with Pool(pool) as p:
- signals = p.map(
- lambda x: concat_signal_ind(path, group_names, x[0], x[1]),
- sitems,
- )
- else:
- signals = [
- concat_signal_ind(path, group_names, name, signal)
- for name, signal in sitems
- ]
-
- signals = [s for s in signals if s is not None]
- sorted = pd.concat(signals, axis=axis).sort_index()
- if reduce_cols:
- sorted = sorted.apply(np.nanmean, axis=1)
- spath = path.split("/")
- sorted.name = "_".join([spath[1], spath[-1]])
-
- return sorted
-
- @property
- def ntraps(self):
- for pos, s in self.signals.items():
- with h5py.File(s.filename, "r") as f:
- print(pos, f["/trap_info/trap_locations"].shape[0])
-
- def traplocs(self):
- d = {}
- for pos, s in self.signals.items():
- with h5py.File(s.filename, "r") as f:
- d[pos] = f["/trap_info/trap_locations"][()]
- return d
-
-
-class MetaGrouper(Grouper):
- """Group positions using metadata's 'group' number"""
-
- pass
-
-
-class NameGrouper(Grouper):
- """
- Group a set of positions using a subsection of the name
- """
-
- def __init__(self, dir, by=None):
- super().__init__(dir=dir)
-
- if by is None:
- by = (0, -4)
- self.by = by
-
- @property
- def group_names(self):
- if not hasattr(self, "_group_names"):
- self._group_names = {}
- for name in self.signals.keys():
- self._group_names[name] = name[self.by[0] : self.by[1]]
-
- return self._group_names
-
- def aggregate_multisignals(self, paths=None, **kwargs):
-
- aggregated = pd.concat(
- [
- self.concat_signal(path, reduce_cols=np.nanmean, **kwargs)
- for path in paths
- ],
- axis=1,
- )
- # ph = pd.Series(
- # [
- # self.ph_from_group(x[list(aggregated.index.names).index("group")])
- # for x in aggregated.index
- # ],
- # index=aggregated.index,
- # name="media_pH",
- # )
- # self.aggregated = pd.concat((aggregated, ph), axis=1)
-
- return aggregated
-
-
-class phGrouper(NameGrouper):
- """
- Grouper for pH calibration experiments where all surveyed media pH values
- are within a single experiment.
- """
-
- def __init__(self, dir, by=(3, 7)):
- super().__init__(dir=dir, by=by)
-
- def get_ph(self):
- self.ph = {gn: self.ph_from_group(gn) for gn in self.group_names}
-
- @staticmethod
- def ph_from_group(group_name):
- if group_name.startswith("ph_"):
- group_name = group_name[3:]
-
- return float(group_name.replace("_", "."))
-
- def aggregate_multisignals(self, paths):
-
- aggregated = pd.concat(
- [self.concat_signal(path, reduce_cols=np.nanmean) for path in paths], axis=1
- )
- ph = pd.Series(
- [
- self.ph_from_group(x[list(aggregated.index.names).index("group")])
- for x in aggregated.index
- ],
- index=aggregated.index,
- name="media_pH",
- )
- aggregated = pd.concat((aggregated, ph), axis=1)
-
- return aggregated
-
-
-def concat_signal_ind(path, group_names, group, signal):
- print("Looking at ", group)
- # try:
- combined = signal[path]
- combined["position"] = group
- combined["group"] = group_names[group]
- combined.set_index(["group", "position"], inplace=True, append=True)
- combined.index = combined.index.swaplevel(-2, 0).swaplevel(-1, 1)
-
- return combined
- # except:
- # return None
diff --git a/poetry.lock b/poetry.lock
index f93587a0..882b485b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -78,13 +78,16 @@ python-versions = "*"
[[package]]
name = "aliby-agora"
-version = "0.2.3"
+version = "0.2.8"
description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
category = "main"
optional = false
python-versions = ">=3.7.1,<3.11"
[package.dependencies]
+h5py = "2.10"
+pandas = ">=1.3.5,<2.0.0"
+py-find-1st = ">=1.1.5,<2.0.0"
PyYAML = ">=6.0,<7.0"
[[package]]
@@ -110,20 +113,21 @@ xgboost = "1.4.2"
[[package]]
name = "aliby-post"
-version = "0.1.1"
+version = "0.1.2"
description = "Post-processing tools for aliby pipeline."
category = "main"
optional = false
python-versions = ">=3.7.1,<3.11"
[package.dependencies]
-aliby-agora = ">=0.2.0"
+aliby-agora = ">=0.2.7,<0.3.0"
catch22 = ">=0.2.0,<0.3.0"
leidenalg = ">=0.8.8,<0.9.0"
more-itertools = ">=8.12.0,<9.0.0"
numpy = ">=1.17.3"
omni-gaussian = "*"
pandas = ">=1.3.5,<2.0.0"
+pathos = ">=0.2.8,<0.3.0"
PyYAML = ">=6.0,<7.0"
scipy = ">=1.4.1"
@@ -1913,7 +1917,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[metadata]
lock-version = "1.1"
python-versions = ">=3.7.1,<3.11"
-content-hash = "e1e7066cb95566d8b8151a3dc7fc74d2dce27c535c55e6acdb708ce6a6b55c19"
+content-hash = "2df95f3e88418a2193aa261bbe8823aea1e3830add76236b5e38e1b98ec740d4"
[metadata.files]
absl-py = [
@@ -2011,16 +2015,16 @@ alabaster = [
{file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
]
aliby-agora = [
- {file = "aliby-agora-0.2.3.tar.gz", hash = "sha256:a3a56a773243c04fb4dffb54301d77ff7869e98047d6ba9261cbe4864f715744"},
- {file = "aliby_agora-0.2.3-py3-none-any.whl", hash = "sha256:003f5b52dfa5513ea02497701c11dd50014496c264de75f474534358df89416b"},
+ {file = "aliby-agora-0.2.8.tar.gz", hash = "sha256:e340e917ff62c7694e174ceb2d0c32f1c8335b501be7af0dc7145058ebd1d5a1"},
+ {file = "aliby_agora-0.2.8-py3-none-any.whl", hash = "sha256:4e02b79d76db6941c55a25f2d0936bc80039f3b63b9bfd94facc07dafd32f363"},
]
aliby-baby = [
{file = "aliby-baby-0.1.2.tar.gz", hash = "sha256:564a12b44fc7e4889fb70d5a82e39e7fb01f37eeb60669c684bd18677160de93"},
{file = "aliby_baby-0.1.2-py3-none-any.whl", hash = "sha256:f8f11b82db89a74ad8cc48059370af889f246a83d4cbc45ce75d9475a15605f7"},
]
aliby-post = [
- {file = "aliby-post-0.1.1.tar.gz", hash = "sha256:426510854767402adc06ed62b7867866dcad054838432ffe26ebb91861c85828"},
- {file = "aliby_post-0.1.1-py3-none-any.whl", hash = "sha256:6bd666a37b83ee750c9837ce08a8541d16290811fadcf020378b6122f3b1f8bd"},
+ {file = "aliby-post-0.1.2.tar.gz", hash = "sha256:73940768cd3bc77908525ec7700c6712f520cb768e505019db644ee391feafc5"},
+ {file = "aliby_post-0.1.2-py3-none-any.whl", hash = "sha256:ed01d4f96ebd24a0832d8f27de4dc38d649609d47507ffa760ff57b255e4fde4"},
]
appdirs = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
diff --git a/pyproject.toml b/pyproject.toml
index b46e1308..114dfd28 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "aliby"
-version = "0.1.7"
+version = "0.1.8"
description = ""
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
@@ -28,10 +28,10 @@ imageio = "2.8.0"
omero-py = ">=5.6.2"
zeroc-ice = "3.6.5"
tensorflow = ">=1.15,<=2.3"
-aliby-agora = ">=0.2.0"
-aliby-baby = "*"
-omni-gaussian = "*"
-aliby-post = "^0.1.1"
+aliby-agora = "^0.2.4"
+aliby-baby = "^0.1.2"
+omni-gaussian = "^0.1.1"
+aliby-post = "^0.1.2"
[tool.poetry.dev-dependencies]
--
GitLab