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 *