Update use of brainglobe-utils image IO (#108)

Co-authored-by: alessandrofelder <[email protected]>

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 (

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 (

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 (

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",