Merge imio in as image_io submodule (#33)

* Initial commit * bump * bump * bump * add bump2version * Bump version: 0.0.2 → 0.0.3 * add pre commit hooks * update testing * reorder ci * fix non-istropic loading error * Bump version: 0.0.3 → 0.0.4 * Gh actions (#3) * add gh actions * Update testing * update testing * add lint * coveralls * coveralls * deploy * Bump version: 0.0.4 → 0.0.5 * update readme * transfer to brainglobe * run tests on PR * update coverage * support python 3.9 * Bump version: 0.0.5 → 0.0.6 * update bump2version * Bump version: 0.0.6 → 0.1.0-rc0 * Bump version: 0.1.0-rc0 → 0.1.0 * Update setup.py * add missing import * Update README.md * fix linting * Exclude tests from packaged distributions (#6) * Update pre commit * reformat * Python 3.10 compatibility * Bump version: 0.1.0 → 0.2.0-rc0 * update GH actions * Bump version: 0.2.0-rc0 → 0.2.0-rc1 * Bump version: 0.2.0-rc1 → 0.2.0 * Revert older changes * Fix deprecation of tifffile.imsave replaced by tifffile.imwrite. (#8) Co-authored-by: Jules Scholler <[email protected]> * Bump version: 0.2.1 → 0.2.2-rc0 * Bump version: 0.2.2-rc0 → 0.2.2 * Add link to contributing guide * Add tox and use brainglobe/actions (#10) * Add tox and use brainglobe actions for testing * Update pre-commit * run pre-commit * Update tox.ini * Bump version: 0.2.2 → 0.2.3-rc0 * Bump version: 0.2.3-rc0 → 0.2.3 * Long description (#11) * Add long description for PyPI * Bump version: 0.2.3 → 0.2.4-rc0 * Bump version: 0.2.4-rc0 → 0.2.4 * Change coverage badge to codecov. * Test on recent python versions (#13) * Test on recent python versions * Bump pre-commit versions * Fix dtype issue * Remove straggling mention of 3.7 * Replace brainglobe > NI actions (#14) * Use standard pre-commit config (#15) * Add standard pre-commit config * pre-commit fixes * Use pyproject.toml (#16) * Filter warnings in pytest (#17) * Filter warnings in pytest * Filter nptyping warnings * Add all-contributors * Update README.md Co-authored-by: David Stansby <[email protected]> * docs: add crousseau as a contributor for code, ideas, and test (#25) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Remove badge --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> * Don't skip CI for all-contrbutors-bot * Update .all-contributorsrc * docs: add jaimergp as a contributor for code (#23) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> * docs: add JulesScholler as a contributor for code (#22) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md * Update .all-contributorsrc * Update .all-contributorsrc --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> * docs: add dstansby as a contributor for test, code, and 3 more (#21) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> * docs: add adamltyson as a contributor for code, infra, and 2 more (#24) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> * Update doc links (#27) * [pre-commit.ci] pre-commit autoupdate (#28) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.240...v0.0.272) - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) - [github.com/pre-commit/mirrors-mypy: v0.991 → v1.3.0](pre-commit/mirrors-mypy@v0.991...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update dependency (imlib -> brainglobe-utils) (#29) * [pre-commit.ci] pre-commit autoupdate (#31) updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275) - [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.4.1](pre-commit/mirrors-mypy@v1.3.0...v1.4.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * remove all contributors (#32) * [pre-commit.ci] pre-commit autoupdate (#33) updates: - https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit - [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#34) updates: - 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[github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.4...v0.1.6) - [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0) - [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.1](pre-commit/mirrors-mypy@v1.6.1...v1.7.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#50) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.6...v0.1.9) - [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1) - [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](pre-commit/mirrors-mypy@v1.7.1...v1.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update GH actions badge (#51) * Update test_and_deploy.yml (#52) See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <[email protected]> * Add manifest (#54) * Update CI workflows with manifest * Allow workflow to be dispatchable * Add pyarrow dependency to prevent future pandas failures * [pre-commit.ci] pre-commit autoupdate (#53) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0) - [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * refactor image_io as submodule * Deprecated alias warning is still present * Fix an actual circular import because of wildcard import * Fix buggy html logo - wrong escape backslash --------- Co-authored-by: crousseau <[email protected]> Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Jaime Rodríguez-Guerra <[email protected]> Co-authored-by: Jules Scholler <[email protected]> Co-authored-by: Jules Scholler <[email protected]> Co-authored-by: David Stansby <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <[email protected]> Co-authored-by: Igor Tatarnikov <[email protected]>
brainglobe · Feb 9, 2024 · 5a2a2d6 · 5a2a2d6
1 parent 6bae0a6
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Showing 12 changed files with 757 additions and 70 deletions.
diff --git a/.github/workflows/test_and_deploy.yml b/.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]

diff --git a/.pre-commit-config.yaml b/.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
diff --git a/README.md b/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]

diff --git a/brainglobe_utils/brainreg/transform.py b/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])

diff --git a/brainglobe_utils/image/heatmap.py b/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
diff --git a/brainglobe_utils/image_io/__init__.py b/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 *