From 2c3ebc4935cd4078593caa338278392c2cd1c030 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Thu, 16 May 2024 13:53:56 +0100 Subject: [PATCH] Update use of brainglobe-utils image IO (#108) Co-authored-by: alessandrofelder --- benchmarks/benchmarks/cellfinder.py | 2 +- brainglobe_workflows/brainmapper/main.py | 2 +- brainglobe_workflows/cellfinder/cellfinder.py | 2 +- pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/benchmarks/benchmarks/cellfinder.py b/benchmarks/benchmarks/cellfinder.py index e3fc06a4..ab576b65 100644 --- a/benchmarks/benchmarks/cellfinder.py +++ b/benchmarks/benchmarks/cellfinder.py @@ -4,8 +4,8 @@ from pathlib import Path from brainglobe_utils.IO.cells import save_cells +from brainglobe_utils.IO.image.load import read_with_dask from cellfinder.core.main import main as cellfinder_run -from cellfinder.core.tools.IO import read_with_dask from cellfinder.core.tools.prep import prep_models from brainglobe_workflows.cellfinder.cellfinder import ( diff --git a/brainglobe_workflows/brainmapper/main.py b/brainglobe_workflows/brainmapper/main.py index df344fdb..22e32cb7 100644 --- a/brainglobe_workflows/brainmapper/main.py +++ b/brainglobe_workflows/brainmapper/main.py @@ -19,6 +19,7 @@ from brainglobe_utils.general.system import ensure_directory_exists from brainglobe_utils.image.heatmap import heatmap_from_points from brainglobe_utils.IO.cells import get_cells, save_cells +from brainglobe_utils.IO.image.load import read_z_stack from cellfinder.core.main import suppress_tf_logging, tf_suppress_log_messages BRAINREG_PRE_PROCESSING_ARGS = None @@ -105,7 +106,6 @@ def run_all(args, what_to_run, atlas): from cellfinder.core.classify import classify from cellfinder.core.detect import detect from cellfinder.core.tools import prep - from cellfinder.core.tools.IO import read_z_stack from brainglobe_workflows.brainmapper import analyse from brainglobe_workflows.brainmapper.prep import ( diff --git a/brainglobe_workflows/cellfinder/cellfinder.py b/brainglobe_workflows/cellfinder/cellfinder.py index 6a0789c5..aca05890 100644 --- a/brainglobe_workflows/cellfinder/cellfinder.py +++ b/brainglobe_workflows/cellfinder/cellfinder.py @@ -25,8 +25,8 @@ import pooch from brainglobe_utils.IO.cells import save_cells +from brainglobe_utils.IO.image.load import read_with_dask from cellfinder.core.main import main as cellfinder_run -from cellfinder.core.tools.IO import read_with_dask from cellfinder.core.train.train_yml import depth_type from brainglobe_workflows.utils import ( diff --git a/pyproject.toml b/pyproject.toml index f828769f..aae15f17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ dependencies = [ "configobj", "fancylog>=0.0.7", "imio", - "brainglobe-utils>=0.2.5", + "brainglobe-utils>=0.5.0", "multiprocessing-logging>=0.3.4", "natsort", "numpy",