image2image-io 0.1.10__tar.gz

image2image_io-0.1.10/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

image2image_io-0.1.10/.github/ISSUE_TEMPLATE.md

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+* image2image-io version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

image2image_io-0.1.10/.github/TEST_FAIL_TEMPLATE.md

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+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

image2image_io-0.1.10/.github/dependabot.yml

@@ -0,0 +1,10 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

image2image_io-0.1.10/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 0" # every week (for --pre release tests)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@v2
+    secrets: inherit
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      pip-install-pre-release: ${{ github.event_name == 'schedule' }}
+      report-failures: ${{ github.event_name == 'schedule' }}
+      extras: 'test'
+      # changing this to "artifact" prevents uploading to codecov here,
+      # instead it uploads an artifact with the coverage data
+      coverage-upload: artifact
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]#, "3.13"]
+        include:
+          - python-version: "3.9"
+            os: ubuntu-latest
+          - python-version: "3.9"
+            os: macos-13
+          - python-version: "3.11"
+            os: macos-latest
+          - python-version: "3.12"
+            os: macos-latest
+
+
+  # now add another job to combine and upload the coverage
+  upload_coverage:
+    if: always()
+    needs: [test]
+    uses: pyapp-kit/workflows/.github/workflows/upload-coverage.yml@v2
+    secrets:
+      codecov_token: ${{ secrets.CODECOV_TOKEN }}
+
+  deploy_test:
+    name: Deploy to PyPI (test)
+    needs: [check-manifest, test]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+
+      - name: Build and publish
+        run: twine upload --repository testpypi dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+
+  deploy:
+    name: Deploy
+    needs: [check-manifest, test, deploy_test]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          git tag
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+
+      - name: Build and publish
+        run: twine upload dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

image2image_io-0.1.10/.github_changelog_generator

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+user=vandeplaslab
+project=image2image-io
+issues=false
+exclude-labels=duplicate,question,invalid,wontfix,hide
+add-sections={"tests":{"prefix":"**Tests & CI:**","labels":["tests"]}, "documentation":{"prefix":"**Documentation:**", "labels":["documentation"]}}
+exclude-tags-regex=.*rc

image2image_io-0.1.10/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+
+_version.py
+
+# nuitka
+*.build/
+
+# idea
+*.iml
+.idea/modules.xml
+.idea/misc.xml
+.idea/workspace.xml
+.idea/watcherTasks.xml
+.idea/vcs.xml
+/.idea

image2image_io-0.1.10/.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+default_install_hook_types: [pre-commit, commit-msg]
+
+repos:
+#  -   repo: https://github.com/pre-commit/pre-commit-hooks
+#      rev: v4.4.0
+#      hooks:
+#      - id: no-commit-to-branch
+#        args: ['--branch', 'master', "--branch", "main"]
+
+  -   repo: https://github.com/MarcoGorelli/absolufy-imports
+      rev: v0.3.1
+      hooks:
+      -   id: absolufy-imports
+          exclude: _vendor|vendored
+
+  -   repo: https://github.com/hadialqattan/pycln
+      rev: v2.1.3
+      hooks:
+      - id: pycln
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+
+  -   repo: https://github.com/psf/black
+      rev: 23.1.0
+      hooks:
+      - id: black
+        pass_filenames: true
+
+  -   repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.252
+      hooks:
+        - id: ruff
+          args: [--fix]
+
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.0.1
+#    hooks:
+#      - id: mypy
+#        files: "^src/"
+#        # # you have to add the things you want to type check against here
+#        # additional_dependencies:
+#        #   - numpy

image2image_io-0.1.10/LICENSE

@@ -0,0 +1,29 @@
+BSD License
+
+Copyright (c) 2023, Lukasz G. Migas
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

image2image_io-0.1.10/Makefile

@@ -0,0 +1,32 @@
+.PHONY: pre watch dist settings-schema untrack
+
+# note: much faster to run mypy as daemon,
+# dmypy run -- ...
+# https://mypy.readthedocs.io/en/stable/mypy_daemon.html
+typecheck:
+	tox -e mypy
+
+check-manifest:
+	pip install -U check-manifest
+	check-manifest
+
+dist: check-manifest
+	pip install -U build
+	python -m build
+
+pre:
+	pre-commit run -a
+
+# If the first argument is "watch"...
+ifeq (watch,$(firstword $(MAKECMDGOALS)))
+  # use the rest as arguments for "watch"
+  WATCH_ARGS := $(wordlist 2,$(words $(MAKECMDGOALS)),$(MAKECMDGOALS))
+  # ...and turn them into do-nothing targets
+  $(eval $(WATCH_ARGS):;@:)
+endif
+
+.PHONY: untrack
+untrack:
+	git rm -r --cached .
+	git add .
+	git commit -m ".gitignore fix"

image2image_io-0.1.10/PKG-INFO

@@ -0,0 +1,176 @@
+Metadata-Version: 2.4
+Name: image2image-io
+Version: 0.1.10
+Summary: Various image readers
+Author-email: "Lukasz G. Migas" <lukas.migas@yahoo.com>
+License: BSD 3-Clause License
+Project-URL: homepage, https://github.com/vandeplaslab/image2image-io
+Project-URL: repository, https://github.com/vandeplaslab/image2image-io
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: zarr
+Requires-Dist: h5py
+Requires-Dist: imzy
+Requires-Dist: czifile
+Requires-Dist: tifffile
+Requires-Dist: imagecodecs
+Requires-Dist: aicsimageio[bioformats]
+Requires-Dist: ome_types
+Requires-Dist: rasterio
+Requires-Dist: shapely
+Requires-Dist: pint
+Requires-Dist: pydantic>=2
+Requires-Dist: scikit-image
+Requires-Dist: SimpleITK
+Requires-Dist: opencv-python
+Requires-Dist: dicttoxml
+Requires-Dist: appdirs
+Requires-Dist: geojson
+Requires-Dist: pyarrow
+Requires-Dist: fastparquet
+Requires-Dist: numcodecs<0.16.0
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: rich; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: image2image-io[test]; extra == "dev"
+Dynamic: license-file
+
+# image2image-io
+
+[![License](https://img.shields.io/pypi/l/image2image-io.svg?color=green)](https://github.com/vandeplaslab/image2image-io/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/image2image-io.svg?color=green)](https://pypi.org/project/image2image-io)
+[![Python Version](https://img.shields.io/pypi/pyversions/image2image-io.svg?color=green)](https://python.org)
+[![CI](https://github.com/vandeplaslab/image2image-io/actions/workflows/ci.yml/badge.svg)](https://github.com/vandeplaslab/image2image-io/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/vandeplaslab/image2image-io/branch/main/graph/badge.svg)](https://codecov.io/gh/vandeplaslab/image2image-io)
+
+## Overview
+
+This library provides reader/writer interface to several popular image formats. The main goal is to give a unified
+interface to access the image data (e.g. for specific channel or pyramid level).
+
+## Getting started
+
+Currently supported formats:
+- Standard image formats (.png, .jpg, .jpeg)
+- TIFF (.tif, .tiff, .ome.tiff, .scn, .svs, .ndpi, .qptiff, .qptiff.raw, .qptiff.intermediate)
+- CZI (.czi)
+- Bruker (.tsf, .tdf, .d)
+- ImzML (.imzML, .ibd)
+- HDF5 (.h5, .hdf5) - specific schema required
+- Numpy (.npy, .npz) - expects 2D or 3D numpy array
+- GeoJSON (.geojson) - expects a dictionary with 'type' and 'features' keys (e.g. from QuPath or GeoPandas)
+- Points (.csv, .txt, .parquet) - specific schema required
+
+If you want to open an image, you can use the `get_simple_reader` function. This function will automatically detect the
+image format and return the appropriate reader.
+
+```python
+from image2image_io.readers import get_simple_reader
+
+# Path to your image
+path_to_image = "path/to/image.ome.tiff"
+
+# Get instance of the reader.
+reader = get_simple_reader(
+    path_to_image, 
+    init_pyramid=True  # initialize the pyramid upon loading the image
+)
+
+# Retrieve the pyramid stack. In this case 'pyramid' is a list of numpy or dask arrays.
+pyramid = reader.pyramid
+
+# Retrieve the first channel of the first pyramid level
+channel_first = reader.get_channel(0, 0)  # channel_id, pyramid_level
+
+# Retrieve the first channel of the last pyramid level
+channel_last = reader.get_channel(0, -1)  # channel_id, pyramid_level
+
+# Writing to file is relatively easy
+reader.to_ome_tiff(
+    'path/to/output.ome.tiff',
+    as_uint8=True,  # will convert the data to uint8
+    tile_size=1024,  # tile size for the output image
+    channel_ids=[0, 2],  # channel ids - specify which channels to write
+    channel_names=['Channel 1', 'Channel 3'],  # channel names - specify the names of the channels
+)
+```
+
+Writing a numpy array to an OME-TIFF file is also possible:
+    
+```python
+import numpy as np
+from image2image_io.writers import write_ome_tiff_from_array
+
+# Create a numpy array
+array = np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8)  # RGB image  
+
+# Write the numpy array to an OME-TIFF file
+write_ome_tiff_from_array(
+    "path/to/output.ome.tiff",
+    None,
+    array,
+    tile_size=1024,  # tile size for the output image
+    channel_names=["R", "G", "B"],  # for RGB images, this might now have any effect
+    resolution=0.5,  # resolution of the image in microns
+)
+```
+
+Merging multiple images is alsy fairly easy to do:
+
+```python
+from image2image_io.writers import merge_images
+
+# Paths to the images
+paths = ["path/to/image1.ome.tiff", "path/to/image2.ome.tiff"]
+
+# Merge the images
+merge_images(
+    "output.ome.tiff",  # filename
+    paths,  # list of paths to the images
+    output_dir="path/to/output/dir",  # output directory for the final image
+    tile_size=1024,  # tile size for the output image
+    metadata={  # metadata for the output image - this specifies which channels to use in the export
+        "path/to/image1.ome.tiff": {
+            0: {
+                "name": "image-1",
+                "channel_ids": [0, 2],
+                "channel_names": ["Channel 1", "Channel 3"],
+                }
+        },
+        "path/to/image2.ome.tiff": {
+            0: {
+                "name": "image-2",
+                "channel_ids": [0, 1],
+                "channel_names": ["Channel 1", "Channel 2"],
+                }
+        }
+    }
+)
+``` 
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/vandeplaslab/image2image-io.git
+
+pip install -e .[dev]
+```

image2image_io-0.1.10/README.md

@@ -0,0 +1,122 @@
+# image2image-io
+
+[![License](https://img.shields.io/pypi/l/image2image-io.svg?color=green)](https://github.com/vandeplaslab/image2image-io/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/image2image-io.svg?color=green)](https://pypi.org/project/image2image-io)
+[![Python Version](https://img.shields.io/pypi/pyversions/image2image-io.svg?color=green)](https://python.org)
+[![CI](https://github.com/vandeplaslab/image2image-io/actions/workflows/ci.yml/badge.svg)](https://github.com/vandeplaslab/image2image-io/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/vandeplaslab/image2image-io/branch/main/graph/badge.svg)](https://codecov.io/gh/vandeplaslab/image2image-io)
+
+## Overview
+
+This library provides reader/writer interface to several popular image formats. The main goal is to give a unified
+interface to access the image data (e.g. for specific channel or pyramid level).
+
+## Getting started
+
+Currently supported formats:
+- Standard image formats (.png, .jpg, .jpeg)
+- TIFF (.tif, .tiff, .ome.tiff, .scn, .svs, .ndpi, .qptiff, .qptiff.raw, .qptiff.intermediate)
+- CZI (.czi)
+- Bruker (.tsf, .tdf, .d)
+- ImzML (.imzML, .ibd)
+- HDF5 (.h5, .hdf5) - specific schema required
+- Numpy (.npy, .npz) - expects 2D or 3D numpy array
+- GeoJSON (.geojson) - expects a dictionary with 'type' and 'features' keys (e.g. from QuPath or GeoPandas)
+- Points (.csv, .txt, .parquet) - specific schema required
+
+If you want to open an image, you can use the `get_simple_reader` function. This function will automatically detect the
+image format and return the appropriate reader.
+
+```python
+from image2image_io.readers import get_simple_reader
+
+# Path to your image
+path_to_image = "path/to/image.ome.tiff"
+
+# Get instance of the reader.
+reader = get_simple_reader(
+    path_to_image, 
+    init_pyramid=True  # initialize the pyramid upon loading the image
+)
+
+# Retrieve the pyramid stack. In this case 'pyramid' is a list of numpy or dask arrays.
+pyramid = reader.pyramid
+
+# Retrieve the first channel of the first pyramid level
+channel_first = reader.get_channel(0, 0)  # channel_id, pyramid_level
+
+# Retrieve the first channel of the last pyramid level
+channel_last = reader.get_channel(0, -1)  # channel_id, pyramid_level
+
+# Writing to file is relatively easy
+reader.to_ome_tiff(
+    'path/to/output.ome.tiff',
+    as_uint8=True,  # will convert the data to uint8
+    tile_size=1024,  # tile size for the output image
+    channel_ids=[0, 2],  # channel ids - specify which channels to write
+    channel_names=['Channel 1', 'Channel 3'],  # channel names - specify the names of the channels
+)
+```
+
+Writing a numpy array to an OME-TIFF file is also possible:
+    
+```python
+import numpy as np
+from image2image_io.writers import write_ome_tiff_from_array
+
+# Create a numpy array
+array = np.random.randint(0, 255, (100, 100, 3), dtype=np.uint8)  # RGB image  
+
+# Write the numpy array to an OME-TIFF file
+write_ome_tiff_from_array(
+    "path/to/output.ome.tiff",
+    None,
+    array,
+    tile_size=1024,  # tile size for the output image
+    channel_names=["R", "G", "B"],  # for RGB images, this might now have any effect
+    resolution=0.5,  # resolution of the image in microns
+)
+```
+
+Merging multiple images is alsy fairly easy to do:
+
+```python
+from image2image_io.writers import merge_images
+
+# Paths to the images
+paths = ["path/to/image1.ome.tiff", "path/to/image2.ome.tiff"]
+
+# Merge the images
+merge_images(
+    "output.ome.tiff",  # filename
+    paths,  # list of paths to the images
+    output_dir="path/to/output/dir",  # output directory for the final image
+    tile_size=1024,  # tile size for the output image
+    metadata={  # metadata for the output image - this specifies which channels to use in the export
+        "path/to/image1.ome.tiff": {
+            0: {
+                "name": "image-1",
+                "channel_ids": [0, 2],
+                "channel_names": ["Channel 1", "Channel 3"],
+                }
+        },
+        "path/to/image2.ome.tiff": {
+            0: {
+                "name": "image-2",
+                "channel_ids": [0, 1],
+                "channel_names": ["Channel 1", "Channel 2"],
+                }
+        }
+    }
+)
+``` 
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/vandeplaslab/image2image-io.git
+
+pip install -e .[dev]
+```