From 2ca1fe19e4edaecd9bb6d3ee0c8589a102cc2ed2 Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Wed, 19 Jul 2023 12:30:00 +0100
Subject: [PATCH] added function to add gr data to dl.df
---
growth_rate.py | 24 +++++++++++++-----------
1 file changed, 13 insertions(+), 11 deletions(-)
diff --git a/growth_rate.py b/growth_rate.py
index b49a8d3..685dccd 100644
--- a/growth_rate.py
+++ b/growth_rate.py
@@ -13,8 +13,8 @@ from wela.figs2pdf import figs2pdf
def find_all_grs(
dataname,
max_no_cells=None,
- indir=None,
- outdir=".",
+ h5dir=None,
+ wdir=".",
use_tsv=True,
):
"""
@@ -26,9 +26,9 @@ def find_all_grs(
Name of experiment, passed to dataloader.
max_no_cells: None or int
The maximum number of cells to process.
- indir: str (optional)
+ h5dir: str (optional)
The directory containing the h5 files.
- outdir: str (optional)
+ wdir: str (optional)
The directory containing any tsv files to load and where tsv
files will be saved.
use_tsv: boolean (optional)
@@ -37,7 +37,7 @@ def find_all_grs(
Example
-------
>>> from wela.growth_rate import find_all_grs
- >>> find_all_grs("Pdr5", max_no_cells=2, outdir="tsv_files")
+ >>> find_all_grs("Pdr5", max_no_cells=2, wdir="tsv_data")
"""
# only save if all cells are processed
if max_no_cells is None:
@@ -45,7 +45,7 @@ def find_all_grs(
else:
save = False
# get data
- dl = dataloader(indir=indir, outdir=outdir)
+ dl = dataloader(h5dir=h5dir, wdir=wdir)
dl.load(dataname, use_tsv=use_tsv)
b_vol = dl.wide_df("bud_volume")
m_vol = dl.wide_df("volume")
@@ -67,10 +67,12 @@ def find_all_grs(
pickle.dump(res_m, open(dataname + "_res_m.pkl", "wb"))
figs2pdf(dataname + "_m.pdf")
plt.close("all")
- # add to dataframe and save
- if save:
- addgrfrompkl(dl, ".")
- dl.save(dataname)
+
+
+def add_to_dataframe(dl, pkl_dir="."):
+ """Add data from pkl files to a dataloader's data frame."""
+ addgrfrompkl(dl, pkl_dir)
+ dl.save(dl.dataname)
def find_gr(
@@ -209,7 +211,7 @@ def runGP(x, y, bounds, noruns, signals, verbose, title, maxnofigs=70):
mg.sketch(".", derivs=1)
plt.ylabel("d/dt volume")
plt.xlabel("time")
- plt.show()
+ plt.show(block=False)
res = dict(
zip(
signals,
--
GitLab