Update dependency (imlib -> brainglobe-utils)

README.md

@@ -8,7 +8,7 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
-[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://docs.brainglobe.info/cellfinder/contributing)
+[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/developers/index.html)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
 # cellfinder-core
@@ -76,7 +76,7 @@ detected_cells = cellfinder_run(signal_array,background_array,voxel_sizes)
 ```
 
 The output is a list of
-[imlib Cell objects](https://github.com/adamltyson/imlib/blob/51ec5a8053e738776ceaa8d44e531b3c4b0e29d8/imlib/cells/cells.py#L15).
+[brainglobe-utils Cell objects](https://github.com/brainglobe/brainglobe-utils/blob/044a735049c1323466d277f9df1c3abad8b2bb8d/brainglobe_utils/cells/cells.py#L19)
 Each `Cell` has a centroid coordinate, and a type:
 
 ```python
@@ -88,7 +88,7 @@ Cell type 2 is a "real" cell, and Cell type 1 is a "rejected" object (i.e.
 not classified as a cell):
 
 ```python
-from imlib.cells.cells import Cell
+from brainglobe_utils.cells.cells import Cell
 print(Cell.CELL)
 # 2
 
@@ -98,15 +98,15 @@ print(Cell.NO_CELL)
 
 #### Saving the results
 If you want to save the detected cells for use in other BrainGlobe software (e.g. the
-[cellfinder napari plugin](https://docs.brainglobe.info/cellfinder-napari/introduction)),
+[cellfinder napari plugin](https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html)),
 you can save in the cellfinder XML standard:
 ```python
-from imlib.IO.cells import save_cells
+from brainglobe_utils.IO.cells import save_cells
 save_cells(detected_cells, "/path/to/cells.xml")
 ```
 You can load these back with:
 ```python
-from imlib.IO.cells import get_cells
+from brainglobe_utils.IO.cells import get_cells
 cells = get_cells("/path/to/cells.xml")
 ```
 
@@ -210,7 +210,8 @@ if len(cell_candidates) > 0: # Don't run if there's nothing to classify
 The training data needed are matched pairs (signal & background) of small
 (usually 50 x 50 x 100um) images centered on the coordinate of candidate cells.
 These can be generated however you like, but I recommend using the
-[Napari plugin](https://docs.brainglobe.info/cellfinder-napari/user-guide/training-data-generation).
+[Napari plugin](https://brainglobe.
+info/documentation/cellfinder/user-guide/napari-plugin/training-data-generation.html).
 
 `cellfinder-core` comes with a 50-layer ResNet trained on ~100,000 data points
 from serial two-photon microscopy images of mouse brains
@@ -296,5 +297,5 @@ If you find this plugin useful, and use it in your research, please cite the pap
 [https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
 **If you use this, or any other tools in the brainglobe suite, please
- [let us know](mailto:[email protected]?subject=cellfinder-core), and
+ [let us know](mailto:[email protected]?subject=cellfinder-core), and
  we'd be happy to promote your paper/talk etc.**

pyproject.toml

@@ -20,7 +20,7 @@ requires-python = ">=3.8"
 dependencies = [
     "dask[array]",
     "fancylog>=0.0.7",
-    "imlib>=0.0.26",
+    "brainglobe-utils",
     "natsort",
     "numba",
     "numpy",
@@ -111,7 +111,7 @@ known-first-party = ["cellfinder_core"]
 [[tool.mypy.overrides]]
 module = [
     "fancylog.*",
-    "imlib.*",
+    "brainglobe_utils.*",
     "natsort.*",
     "numba.*",
     "tensorflow.*",

src/cellfinder_core/classify/classify.py

@@ -2,8 +2,8 @@
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import numpy as np
-from imlib.cells.cells import Cell
-from imlib.general.system import get_num_processes
+from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.system import get_num_processes
 from tensorflow import keras
 
 from cellfinder_core import logger, types

src/cellfinder_core/classify/cube_generator.py

@@ -4,8 +4,8 @@
 
 import numpy as np
 import tensorflow as tf
-from imlib.cells.cells import Cell, group_cells_by_z
-from imlib.general.numerical import is_even
+from brainglobe_utils.cells.cells import Cell, group_cells_by_z
+from brainglobe_utils.general.numerical import is_even
 from scipy.ndimage import zoom
 from skimage.io import imread
 from tensorflow.keras.utils import Sequence

src/cellfinder_core/detect/detect.py

@@ -20,8 +20,8 @@
 from typing import Callable, List, Optional, Sequence, Tuple, TypeVar
 
 import numpy as np
-from imlib.cells.cells import Cell
-from imlib.general.system import get_num_processes
+from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.system import get_num_processes
 
 from cellfinder_core import logger, types
 from cellfinder_core.detect.filters.plane import TileProcessor

src/cellfinder_core/detect/filters/volume/volume_filter.py

@@ -5,7 +5,7 @@
 from typing import Any, Callable, List, Optional, Tuple
 
 import numpy as np
-from imlib.cells.cells import Cell
+from brainglobe_utils.cells.cells import Cell
 from tifffile import tifffile
 from tqdm import tqdm
 

src/cellfinder_core/download/download.py

@@ -3,8 +3,8 @@
 import tarfile
 import urllib.request
 
-from imlib.general.config import get_config_obj
-from imlib.general.system import disk_free_gb
+from brainglobe_utils.general.config import get_config_obj
+from brainglobe_utils.general.system import disk_free_gb
 
 from cellfinder_core.tools.source_files import (
     source_config_cellfinder,

src/cellfinder_core/main.py

@@ -6,7 +6,7 @@
 from typing import Callable, List, Optional, Tuple
 
 import numpy as np
-from imlib.general.logging import suppress_specific_logs
+from brainglobe_utils.general.logging import suppress_specific_logs
 
 from cellfinder_core import logger
 from cellfinder_core.download.models import model_type

src/cellfinder_core/tools/IO.py

@@ -3,9 +3,9 @@
 from typing import Tuple
 
 import numpy as np
+from brainglobe_utils.general.system import get_sorted_file_paths
 from dask import array as da
 from dask import delayed
-from imlib.general.system import get_sorted_file_paths
 from tifffile import TiffFile, imread
 
 

src/cellfinder_core/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):

src/cellfinder_core/tools/prep.py

@@ -7,8 +7,8 @@
 from pathlib import Path
 from typing import Optional
 
-from imlib.general.config import get_config_obj
-from imlib.general.system import get_num_processes
+from brainglobe_utils.general.config import get_config_obj
+from brainglobe_utils.general.system import get_num_processes
 
 import cellfinder_core.tools.tf as tf_tools
 from cellfinder_core import logger

src/cellfinder_core/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):

src/cellfinder_core/tools/tiff.py

@@ -2,7 +2,7 @@
 from os.path import isfile, join
 
 import natsort
-from imlib.cells.cells import Cell, UntypedCell
+from brainglobe_utils.cells.cells import Cell, UntypedCell
 
 
 class TiffList(object):

src/cellfinder_core/train/train_yml.py

@@ -18,11 +18,14 @@
 from pathlib import Path
 from typing import Dict, Literal
 
+from brainglobe_utils.general.numerical import (
+    check_positive_float,
+    check_positive_int,
+)
+from brainglobe_utils.general.system import ensure_directory_exists
+from brainglobe_utils.IO.cells import find_relevant_tiffs
+from brainglobe_utils.IO.yaml import read_yaml_section
 from fancylog import fancylog
-from imlib.general.numerical import check_positive_float, check_positive_int
-from imlib.general.system import ensure_directory_exists
-from imlib.IO.cells import find_relevant_tiffs
-from imlib.IO.yaml import read_yaml_section
 from sklearn.model_selection import train_test_split
 
 import cellfinder_core as program_for_log

tests/tests/test_integration/test_detection.py

@@ -1,10 +1,10 @@
 import os
 from math import isclose
 
-import imlib.IO.cells as cell_io
+import brainglobe_utils.IO.cells as cell_io
 import numpy as np
 import pytest
-from imlib.general.system import get_num_processes
+from brainglobe_utils.general.system import get_num_processes
 
 from cellfinder_core.main import main
 from cellfinder_core.tools.IO import read_with_dask

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_core.tools.system as system