From c696b4aa1e509b6485f7468cc5de5b389322dded Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Tue, 6 Feb 2024 14:48:41 +0000
Subject: [PATCH] refactor(run_gr): renamed batch to multiprocess
---
examples/run_gr.py | 8 ++++----
growth_rate.py | 16 ++++++++--------
2 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/examples/run_gr.py b/examples/run_gr.py
index 61f60c7..159dbca 100644
--- a/examples/run_gr.py
+++ b/examples/run_gr.py
@@ -14,11 +14,11 @@ datasets = [
# 1. It is better to run dataloader first to generate a tsv file.
# Alternatively, to run directly on h5 files, add use_tsv=False.
-# 2. First run with run_GP = True, batch=False, and max_no_cells = 20
+# 2. First run with run_GP = True, multiprocess=False, and max_no_cells = 20
# to check visually the results.
-# 3. Then run with max_no_cells=None and batch=True for multiprocessing.
+# 3. Then run with max_no_cells=None and multiprocess=True for multiprocessing.
# The results are saved in a pkl file.
-# No figures are produced unless batch=False.
+# No figures are produced unless multiprocess=False.
# Any figures are saved in a pdf file.
# 4. Finally run with run_GP = False.
# This load the pkl file and integrates into dataloader's data frame.
@@ -32,7 +32,7 @@ for dataname in datasets:
dataname,
max_no_cells=20,
wdir=wdir,
- batch=False,
+ multiprocess=False,
convert_to_hours=False,
mother_bounds={1: (1, 6), 2: (-1, 4)},
)
diff --git a/growth_rate.py b/growth_rate.py
index 885048c..9b65462 100644
--- a/growth_rate.py
+++ b/growth_rate.py
@@ -20,7 +20,7 @@ def find_all_grs(
use_tsv=True,
bud_bounds=None,
mother_bounds=None,
- batch=False,
+ multiprocess=False,
convert_to_hours=True,
):
"""
@@ -45,7 +45,7 @@ def find_all_grs(
mother_bounds: dict, optional
To change bounds on the hyperparameters for the Gaussian process
applied to mothers.
- batch: boolean, optional
+ multiprocess: boolean, optional
If True, use multiprocessing, but no plots are then produced.
convert_to_hours: boolean
If True, divide time values by 60.
@@ -78,7 +78,7 @@ def find_all_grs(
buddings,
max_no_cells=max_no_cells,
bounds=bud_bounds,
- batch=batch,
+ multiprocess=multiprocess,
convert_to_hours=convert_to_hours,
)
if save:
@@ -91,7 +91,7 @@ def find_all_grs(
m_vol,
max_no_cells=max_no_cells,
bounds=mother_bounds,
- batch=batch,
+ multiprocess=multiprocess,
convert_to_hours=convert_to_hours,
)
if save:
@@ -107,7 +107,7 @@ def find_gr(
bounds=None,
noruns=10,
verbose=True,
- batch=False,
+ multiprocess=False,
max_no_cells=None,
convert_to_hours=True,
):
@@ -158,9 +158,9 @@ def find_gr(
else:
no_cells = volume.shape[0]
# loop over cells
- if batch:
+ if multiprocess:
config["verbose"] = False
- res = run_batch(t, volume, buddings_df, buddings, no_cells, config)
+ res = run_parallel(t, volume, buddings_df, buddings, no_cells, config)
else:
res = run_series(t, volume, buddings_df, buddings, no_cells, config)
# convert results into dataframes
@@ -215,7 +215,7 @@ def run_series(t, volume, buddings_df, buddings, no_cells, config):
return res
-def run_batch(t, volume, buddings_df, buddings, no_cells, config):
+def run_parallel(t, volume, buddings_df, buddings, no_cells, config):
"""
Use multiprocessing to speed GPs.
--
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