Merge imio in as image_io submodule

.github/workflows/test_and_deploy.yml

@@ -3,14 +3,15 @@ name: tests
 on:
  push:
  branches:
- - 'main'
+ - "main"
  tags:
- - 'v*'
+ - "v**"
  pull_request:
  workflow_dispatch:
 
 jobs:
  linting:
+ name: Check Linting
  runs-on: ubuntu-latest
  steps:
  - uses: neuroinformatics-unit/actions/lint@v2
@@ -60,7 +61,6 @@ jobs:
  steps:
  - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
 
-
  upload_all:
  name: Publish build distributions
  needs: [build_sdist_wheels]

.pre-commit-config.yaml

@@ -28,4 +28,7 @@ repos:
  hooks:
  - id: mypy
  args: [--config-file, pyproject.toml]
- additional_dependencies: [numpy]
+ additional_dependencies:
+ - numpy
+ - types-setuptools
+ - types-requests

README.md

@@ -1,17 +1,21 @@
 # brainglobe-utils
+
 Shared general purpose tools for the BrainGlobe project
 
 ## Installation
 
 ```bash
 pip install brainglobe-utils
 ```
+
 To also include the dependencies required for `napari`, use:
+
 ```bash
 pip install brainglobe-utils[napari]
 ```
 
 For development, clone this repository and install the dependencies with one of the following commands:
+
 ```bash
 pip install -e .[dev]
 pip install -e .[dev,napari]

brainglobe_utils/brainreg/transform.py

@@ -2,13 +2,14 @@
 import os
 from typing import List, Optional, Tuple
 
-import bg_space as bgs
-import imio
+import brainglobe_space as bgs
 import numpy as np
 import pandas as pd
 import tifffile
 from bg_atlasapi import BrainGlobeAtlas
 
+from brainglobe_utils.image_io import get_size_image_from_file_paths
+
 
 def transform_points_from_downsampled_to_atlas_space(
  downsampled_points: np.ndarray,
@@ -91,7 +92,7 @@ def get_anatomical_space_from_image_planes(
  image_plane : np.ndarray
  A numpy-like array representing a single image plane from a 3D image.
  orientation : str
- The orientation of the image following the bg-space
+ The orientation of the image following the brainglobe-space
  three-letter convention (e.g., 'asr', 'psl').
  voxel_sizes : List[float]
  A list of floats representing the voxel sizes (e.g., [5, 2, 2]).
@@ -103,7 +104,7 @@ def get_anatomical_space_from_image_planes(
 
  """
 
- shape = tuple(imio.get_size_image_from_file_paths(image_plane).values())
+ shape = tuple(get_size_image_from_file_paths(image_plane).values())
 
  space = bgs.AnatomicalSpace(
  orientation,
@@ -132,7 +133,7 @@ def transform_points_from_raw_to_downsampled_space(
  source_image_plane : np.ndarray
  A numpy-like array representing a single image.
  orientation : str
- The orientation of the image following the bg-space
+ The orientation of the image following the brainglobe-space
  three letter convention (e.g. 'asr', 'psl')
  voxel_sizes : List[float]
  A list of floats representing the voxel sizes (e.g. [5, 2, 2])
@@ -182,7 +183,7 @@ def transform_points_to_atlas_space(
  source_image_plane : np.ndarray
  A numpy-like array representing a single image.
  orientation : str
- The orientation of the image following the bg-space
+ The orientation of the image following the brainglobe-space
  three letter convention (e.g. 'asr', 'psl')
  voxel_sizes : List[float]
  A list of floats representing the voxel sizes (e.g. [5, 2, 2])

brainglobe_utils/image/heatmap.py

@@ -1,7 +1,6 @@
 from pathlib import Path
 from typing import Tuple, Union
 
-import imio
 import numpy as np
 from scipy.ndimage import zoom
 from skimage.filters import gaussian
@@ -10,6 +9,7 @@
 from brainglobe_utils.image.binning import get_bins
 from brainglobe_utils.image.masking import mask_image_threshold
 from brainglobe_utils.image.scale import scale_and_convert_to_16_bits
+from brainglobe_utils.image_io import to_tiff
 
 
 def rescale_array(source_array, target_array, order=1):
@@ -104,6 +104,6 @@ def heatmap_from_points(
 
  if output_filename is not None:
  ensure_directory_exists(Path(output_filename).parent)
- imio.to_tiff(heatmap_array, output_filename)
+ to_tiff(heatmap_array, output_filename)
 
  return heatmap_array

brainglobe_utils/image_io/__init__.py

@@ -0,0 +1,6 @@
+__author__ = "Charly Rousseau, Adam Tyson"
+__version__ = "0.2.4"
+
+from brainglobe_utils.image_io.load import *
+from brainglobe_utils.image_io.save import *
+from brainglobe_utils.image_io.utils import *