Update dependency (imlib -> brainglobe-utils) (#231)

cellfinder/analyse/analyse.py

@@ -15,8 +15,8 @@
 import pandas as pd
 import tifffile
 from bg_atlasapi import BrainGlobeAtlas
-from imlib.general.system import ensure_directory_exists
-from imlib.pandas.misc import sanitise_df
+from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_utils.pandas.misc import sanitise_df
 
 from cellfinder.export.export import export_points
 

cellfinder/extract/extract_cubes.py

@@ -14,9 +14,9 @@
 from math import floor
 
 import numpy as np
-from imlib.cells.cells import group_cells_by_z
-from imlib.general.numerical import is_even
-from imlib.general.system import get_num_processes
+from brainglobe_utils.cells.cells import group_cells_by_z
+from brainglobe_utils.general.numerical import is_even
+from brainglobe_utils.general.system import get_num_processes
 from numpy.linalg.linalg import LinAlgError
 from skimage import transform
 from tifffile import tifffile

cellfinder/figures/heatmap.py

@@ -5,9 +5,9 @@
 import numpy as np
 import pandas as pd
 import tifffile
-from imlib.general.system import ensure_directory_exists
-from imlib.image.masking import mask_image_threshold
-from imlib.image.scale import scale_and_convert_to_16_bits
+from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_utils.image.masking import mask_image_threshold
+from brainglobe_utils.image.scale import scale_and_convert_to_16_bits
 from skimage.filters import gaussian
 
 

cellfinder/main.py

@@ -14,10 +14,10 @@
 
 import bg_space as bgs
 import tifffile
+from brainglobe_utils.cells.cells import MissingCellsError
+from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_utils.IO.cells import get_cells, save_cells
 from cellfinder_core.main import suppress_tf_logging, tf_suppress_log_messages
-from imlib.cells.cells import MissingCellsError
-from imlib.general.system import ensure_directory_exists
-from imlib.IO.cells import get_cells, save_cells
 
 BRAINREG_PRE_PROCESSING_ARGS = None
 

cellfinder/tools/image_processing.py

@@ -1,5 +1,5 @@
 import numpy as np
-from imlib.general.numerical import is_even
+from brainglobe_utils.general.numerical import is_even
 
 
 def crop_center_2d(img, crop_x=None, crop_y=None):

cellfinder/tools/parser.py

@@ -12,14 +12,17 @@
     ArgumentTypeError,
 )
 
+from brainglobe_utils.general.numerical import (
+    check_positive_float,
+    check_positive_int,
+)
 from brainreg.cli import atlas_parse, geometry_parser, niftyreg_parse
 from brainreg.cli import backend_parse as brainreg_backend_parse
 from cellfinder_core.download.cli import (
     download_directory_parser,
     model_parser,
 )
 from cellfinder_core.tools.source_files import source_custom_config_cellfinder
-from imlib.general.numerical import check_positive_float, check_positive_int
 
 from cellfinder import __version__
 

cellfinder/tools/prep.py

@@ -12,10 +12,10 @@
 from pathlib import PurePath
 
 from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_utils.general.exceptions import CommandLineInputError
+from brainglobe_utils.general.system import ensure_directory_exists
 from brainreg.paths import Paths as BrainRegPaths
 from fancylog import fancylog
-from imlib.general.exceptions import CommandLineInputError
-from imlib.general.system import ensure_directory_exists
 
 import cellfinder as program_for_log
 import cellfinder.tools.parser as parser

cellfinder/tools/system.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from imlib.general.exceptions import CommandLineInputError
+from brainglobe_utils.general.exceptions import CommandLineInputError
 
 
 def get_subdirectories(directory, names_only=False):

cellfinder/train/curation.py

@@ -4,11 +4,11 @@
 import napari
 import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.system import get_sorted_file_paths
+from brainglobe_utils.IO.cells import save_cells
 from brainreg.paths import Paths as BrainregPaths
 from brainreg_segment.layout.gui_elements import add_button
-from imlib.cells.cells import Cell
-from imlib.general.system import get_sorted_file_paths
-from imlib.IO.cells import save_cells
 from napari.utils.io import magic_imread
 from napari_cellfinder.cellfinder import get_cell_arrays
 from qtpy import QtCore

cellfinder/train/curation_old.py

@@ -3,11 +3,14 @@
 
 import napari
 import numpy as np
-from imlib.cells.cells import Cell
-from imlib.general.list import unique_elements_lists
-from imlib.general.system import ensure_directory_exists, get_sorted_file_paths
-from imlib.IO.cells import cells_xml_to_df, get_cells, save_cells
-from imlib.IO.yaml import save_yaml
+from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.list import unique_elements_lists
+from brainglobe_utils.general.system import (
+    ensure_directory_exists,
+    get_sorted_file_paths,
+)
+from brainglobe_utils.IO.cells import cells_xml_to_df, get_cells, save_cells
+from brainglobe_utils.IO.yaml import save_yaml
 from napari.utils.io import magic_imread
 from qtpy.QtWidgets import QApplication
 

setup.py

@@ -12,7 +12,7 @@
     "configobj",
     "fancylog>=0.0.7",
     "imio",
-    "imlib>=0.0.26",
+    "brainglobe-utils",
     "multiprocessing-logging>=0.3.4",
     "natsort",
     "numpy",

tests/tests/conftest.py

@@ -2,8 +2,8 @@
 import sys
 
 import pytest
+from brainglobe_utils.general.config import get_config_obj
 from cellfinder_core.download.cli import main as cellfinder_download
-from imlib.general.config import get_config_obj
 
 test_data_dir = pathlib.Path(__file__) / ".." / ".." / "data"
 data_dir = test_data_dir / "brain"

tests/tests/test_integration/test_detection.py

@@ -2,7 +2,7 @@
 import sys
 from math import isclose
 
-import imlib.IO.cells as cell_io
+import brainglobe_utils.IO.cells as cell_io
 import pytest
 
 from cellfinder.main import main as cellfinder_run

tests/tests/test_integration/test_extract.py

@@ -3,12 +3,12 @@
 import imio
 import numpy as np
 import pytest
-from imlib.cells.cells import Cell
-from imlib.general.system import (
+from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.system import (
     delete_directory_contents,
     get_sorted_file_paths,
 )
-from imlib.IO.cells import get_cells
+from brainglobe_utils.IO.cells import get_cells
 from tifffile import tifffile
 
 import cellfinder.extract.extract_cubes as extract_cubes

tests/tests/test_unit/test_tools/test_prep.py

@@ -1,7 +1,7 @@
 import os
 
 import pytest
-from imlib.general.exceptions import CommandLineInputError
+from brainglobe_utils.general.exceptions import CommandLineInputError
 
 from cellfinder.tools import prep
 

tests/tests/test_unit/test_tools/test_system.py

@@ -3,8 +3,8 @@
 from pathlib import Path
 
 import pytest
-from imlib.general.exceptions import CommandLineInputError
-from imlib.general.system import ensure_directory_exists
+from brainglobe_utils.general.exceptions import CommandLineInputError
+from brainglobe_utils.general.system import ensure_directory_exists
 
 import cellfinder.tools.system as system