easyidp 2.0.0.dev3__tar.gz → 2.0.1__tar.gz

easyidp-2.0.1/.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

easyidp-2.0.1/.github/workflows/pytest.yml

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+name: pytest
+
+on:
+  push:
+    branches: [ v2.0 ]
+  pull_request:
+    branches: [ v2.0 ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install project + test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e . --group test
+
+    - name: Download TestData
+      run: | 
+        python ./tests/__init__.py
+    - name: Run pytest
+      run: | 
+        pytest -n auto

easyidp-2.0.1/.github/workflows/uv-publish.yml

@@ -0,0 +1,34 @@
+# copied and modified from: https://blog.ringsaturn.me/amp/posts/better-python-project-maintenance/
+name: publish by uv
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: PyPI
+      url: https://pypi.org/p/easyidp
+    permissions:
+      id-token: write
+    env:
+      TRUSTED_PUBLISHING: always
+    steps:
+      - name: Checkout Actions
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+      - name: nv venv create
+        run: uv sync
+      - name: uv build
+        run: uv build
+      - name: uv publish
+        run: uv publish

easyidp-2.0.1/.gitignore

@@ -0,0 +1,18 @@
+__pycache__
+d
+*.mo
+*.DS_Store
+.archive/*
+.idea/*
+.ipynb_checkpoints/*
+.pytest_cache/*
+.vscode/*
+_install.md
+build/*
+docs/_build/*
+docs/jupyter/.ipynb_checkpoints/*
+dist/*
+easyidp.egg-info/*
+dev.notes/*
+tests/out/*
+.pypirc

easyidp-2.0.1/.python-version

@@ -0,0 +1 @@
+3.10

easyidp-2.0.1/.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+  jobs:
+    install:
+     - python -m pip install --upgrade pip
+     - pip install .
+     - pip install --group docs
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf

easyidp-2.0.0.dev3/README.md → easyidp-2.0.1/PKG-INFO

@@ -1,202 +1,129 @@
-<div align="center">
-
-<p>
-   <!-- <a align="left" href="https://ultralytics.com/yolov5" target="_blank"> -->
-   <img width="850" src="https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/raw/v2.0/docs/_static/images/header_v2.0.png"></a>
-</p>
-
-<p align="center">
-  <img alt="GitHub code size in bytes" src="https://img.shields.io/tokei/lines/github/UTokyo-FieldPhenomics-Lab/EasyIDP?style=plastic">
-  <img alt="GitHub" src="https://img.shields.io/github/license/UTokyo-FieldPhenomics-Lab/EasyIDP?style=plastic">
-  <img alt="GitHub top language" src="https://img.shields.io/github/languages/top/UTokyo-FieldPhenomics-Lab/EasyIDP?style=plastic">
-  <img alt="GitHub Downloads" src="https://img.shields.io/github/downloads/UTokyo-FieldPhenomics-Lab/EasyIDP/total?label=github%20downloads&style=plastic">
-  <img alt="GitHub Downloads" src="https://img.shields.io/pypi/dm/easyidp?color=%233775A9&label=pypi%20downloads&style=plastic">
-</p>
-
-<a href="README_CN.md">中文</a>
-
-</div>
-
-EasyIDP (Easy Intermediate Data Processor), A handy tool for dealing with region of interest (ROI) on the image reconstruction (Metashape & Pix4D) outputs, mainly in agriculture applications. It provides the following functions: 
-
-1. Backward Projection ROI to original images (`Backward Projector`).
-2. Crop ROI on GeoTiff Maps (DOM & DSM) and Point Cloud (`ROI Cropper`).
-3. Save cropped results to corresponding files (`ROI Saver`).
-
-This project tried to use packges based on pure-python, instead of installing some heavy packages (Open3D, OpenCV) and hard to install packages (GDAL dependices) for one or two individual functions. This may cause efficiency loss and differences in coding habit.
-
-## <div align="center">Documentation</div>
-
-Please check [Official Documents](https://easyidp.readthedocs.io/en/latest/) for full documentations. And please also use the [Github Discussion](https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/discussions) when you meet any problems.
-
-
-## <div align="center">Quick Start Examples (Processing)</div>
-
-You can install the packages by PyPi:
-
-```bash
-pip install easyidp
-```
-
-And import the packages in your python code:
-
-```python
-import easyidp as idp
-```
-
----
-
-Before doing the following example, please understand the basic pipeline for image 3D reconstruction by Pix4D or Metashape. And know how to export the DOM, DSM (\*.tiff), and Point cloud (\*.ply). Also require some basic knowledge about GIS shapefile format (\*.shp).
-
-> Please note, if you see this sentence, it means the following examples are not suppported yet.
-
-<details close>
-<summary>1. Read ROI</summary>
-
-```python
-roi = idp.ROI("xxxx.shp")  # lon and lat 2D info
-  
-# get z values from DSM
-roi.get_z_from_dsm("xxxx_dsm.tiff")  # add height 3D info
-```
-
-The 2D roi can be used to crop the DOM, DSM, and point cloud (`2.crop by ROI`). While the 3D roi can be used for Backward projection (`4. Backward projection`)
-</details>
-
-<details close>
-<summary>2. Crop by ROI</summary>
-
-Read the DOM and DSM Geotiff Maps
-```python
-dom = idp.GeoTiff("xxx_dom.tif")
-dsm = idp.GeoTiff("xxx_dsm.tif")
-```
-  
-Read point cloud data
-```python
-ply = idp.PointCloud("xxx_pcd.ply")
-```
-  
-crop the region of interest from ROI:
-```python
-dom_parts = roi.crop(dom)
-dsm_parts = roi.crop(dsm)
-pcd_parts = roi.crop(ply)
-```
-
-If you want to save these crops to given folder:
-```python
-dom_parts = roi.crop(dom, save_folder="./crop_dom")
-dsm_parts = roi.crop(dsm, save_folder="./crop_dsm")
-pcd_parts = roi.crop(ply, save_folder="./crop_pcd")
-```
-
-  
-</details>
-
-<details close>
-<summary>3. Read Reconstruction projects</summary>
-
-Add the reconstruction projects to processing pools (different flight time for the same field):
-  
-```python
-proj = idp.ProjectPool()
-proj.add_pix4d(["date1.p4d", "date2.p4d", ...])
-proj.add_metashape(["date1.psx", "date2.psx", ...])
-```
-
-Then you can specify each chunk by:
-
-```python
-p1 = proj[0]
-# or
-p1 = proj["chunk_or_project_name"]
-```
-
-</details>
-
-<details close>
-<summary>4. Backward Projection</summary>
-  
-```python
->>> img_dict = roi.back2raw(chunk1)
-```
-  
-Then check the results:
-```python
-# find the raw image name list
->>> img_dict.keys()   
-dict_keys(['DJI_0177.JPG', 'DJI_0178.JPG', 'DJI_0179.JPG', 'DJI_0180.JPG', ... ]
-
-# the roi pixel coordinate on that image
->>> img_dict['DJI_0177.JPG'] 
-array([[ 779,  902],
-       [1043,  846],
-       [1099, 1110],
-       [ 834, 1166],
-       [ 779,  902]])
-```
-
-Save backward projected images
-
-```python
-img_dict = roi.back2raw(chunk1, save_folder="folder/to/put/results/")
-```
-
-</details>
-
-## <div align="center">References</div>
-
-Please cite this paper if this project helps you：
-
-```latex
-@Article{wang_easyidp_2021,
-AUTHOR = {Wang, Haozhou and Duan, Yulin and Shi, Yun and Kato, Yoichiro and Ninomiya, Seish and Guo, Wei},
-TITLE = {EasyIDP: A Python Package for Intermediate Data Processing in UAV-Based Plant Phenotyping},
-JOURNAL = {Remote Sensing},
-VOLUME = {13},
-YEAR = {2021},
-NUMBER = {13},
-ARTICLE-NUMBER = {2622},
-URL = {https://www.mdpi.com/2072-4292/13/13/2622},
-ISSN = {2072-4292},
-DOI = {10.3390/rs13132622}
-}
-```
-
-We also thanks the benefits from the following open source projects:
-
-* package main (**for users**)
-  * numpy: [https://numpy.org/](https://numpy.org/)
-  * matplotlib:[https://matplotlib.org/](https://matplotlib.org/)
-  * pillow: [https://github.com/python-pillow/Pillow](https://github.com/python-pillow/Pillow)
-  * pyproj: [https://github.com/pyproj4/pyproj](https://github.com/pyproj4/pyproj)
-  * tifffile: [https://github.com/cgohlke/tifffile](https://github.com/cgohlke/tifffile)
-  * imagecodecs: [https://github.com/cgohlke/imagecodecs](https://github.com/cgohlke/imagecodecs)
-  * shapely: [https://github.com/shapely/shapely](https://github.com/shapely/shapely)
-  * laspy/lasrs/lasio: [https://github.com/laspy/laspy](https://github.com/laspy/laspy)
-  * plyfile: [https://github.com/dranjan/python-plyfile](https://github.com/dranjan/python-plyfile)
-  * pyshp: [https://github.com/GeospatialPython/pyshp](https://github.com/GeospatialPython/pyshp)
-  * tabulate: [https://github.com/astanin/python-tabulate](https://github.com/astanin/python-tabulate)
-  * tqdm: [https://github.com/tqdm/tqdm](https://github.com/tqdm/tqdm)
-  * gdown: [https://github.com/wkentaro/gdown](https://github.com/wkentaro/gdown)
-* package documentation (**for developers**)
-  * sphinx: [https://github.com/sphinx-doc/sphinx](https://github.com/sphinx-doc/sphinx)
-  * nbsphinx: [https://github.com/spatialaudio/nbsphinx](https://github.com/spatialaudio/nbsphinx)
-  * sphinx-gallery: [https://github.com/sphinx-gallery/sphinx-gallery](https://github.com/sphinx-gallery/sphinx-gallery)
-  * sphinx-inline-tabs: [https://github.com/pradyunsg/sphinx-inline-tabs](https://github.com/pradyunsg/sphinx-inline-tabs)
-  * sphinx-intl: [https://github.com/sphinx-doc/sphinx-intl](https://github.com/sphinx-doc/sphinx-intl)
-  * sphinx-rtc-theme: [https://github.com/readthedocs/sphinx_rtd_theme](https://github.com/readthedocs/sphinx_rtd_theme)
-  * furo: [https://github.com/pradyunsg/furo](https://github.com/pradyunsg/furo)
-* package testing and releasing (**for developers**)
-  * pytest: [https://github.com/pytest-dev/pytest](https://github.com/pytest-dev/pytest)
-  * packaging: [https://github.com/pypa/packaging](https://github.com/pypa/packaging)
-  * wheel: [https://github.com/pypa/wheel](https://github.com/pypa/wheel)
-
-This project was partially funded by:
-
-* the JST AIP Acceleration Research “Studies of CPS platform to raise big-data-driven AI agriculture”; 
-* the SICORP Program JPMJSC16H2; 
-* CREST Programs JPMJCR16O2 and JPMJCR16O1; 
-* the International Science & Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAASTIP); 
-* the National Natural Science Foundation of China U19A2061.
+Metadata-Version: 2.4
+Name: easyidp
+Version: 2.0.1
+Summary: A handy tool for dealing with region of interest (ROI) on the image reconstruction (Metashape & Pix4D) outputs, mainly in agriculture applications
+Project-URL: documentation, https://easyidp.readthedocs.io/en/latest/
+Project-URL: source, https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP
+Project-URL: issues, https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/issues
+Project-URL: forum, https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/discussions
+Author-email: Haozhou Wang <howcanoewang@gmail.com>
+License: MIT
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: GIS
+Requires-Python: >=3.10
+Requires-Dist: chardet>=5.2.0
+Requires-Dist: gdown>=5.2.0
+Requires-Dist: geojson>=3.2.0
+Requires-Dist: imagecodecs>=2025.3.30
+Requires-Dist: laspy>=2.5.4
+Requires-Dist: lazrs>=0.6.3
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: numpy>=2.2.5
+Requires-Dist: plyfile>=1.1
+Requires-Dist: pyproj>=3.7.1
+Requires-Dist: pyshp>=2.3.1
+Requires-Dist: scikit-image>=0.25.2
+Requires-Dist: shapely>=2.1.0
+Requires-Dist: tabulate>=0.9.0
+Requires-Dist: tifffile>=2025.5.10
+Requires-Dist: tqdm>=4.67.1
+Description-Content-Type: text/markdown
+
+<div align="center">
+
+<p>
+   <!-- <a align="left" href="https://ultralytics.com/yolov5" target="_blank"> -->
+   <img width="850" src="https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/raw/v2.0/docs/_static/images/header_v2.0.png"></a>
+</p>
+
+<p align="center">
+  <img alt="GitHub Actions Badge" src="https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/actions/workflows/pytest.yml/badge.svg?style=plastic">
+  <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/easyidp?style=plastic">
+  <img alt="GitHub" src="https://img.shields.io/github/license/UTokyo-FieldPhenomics-Lab/EasyIDP?style=plastic">
+  <img alt="GitHub top language" src="https://img.shields.io/github/languages/top/UTokyo-FieldPhenomics-Lab/EasyIDP?style=plastic">
+  <img alt="GitHub Downloads" src="https://img.shields.io/github/downloads/UTokyo-FieldPhenomics-Lab/EasyIDP/total?label=github%20downloads&style=plastic">
+  <img alt="GitHub Downloads" src="https://img.shields.io/pypi/dm/easyidp?color=%233775A9&label=pypi%20downloads&style=plastic">
+</p>
+
+</div>
+
+EasyIDP (Easy Intermediate Data Processor), A handy tool for dealing with region of interest (ROI) on the image reconstruction (Metashape & Pix4D) outputs, mainly in agriculture applications. It provides the following functions: 
+
+1. Backward Projection ROI to original images (`Backward Projector`).
+2. Crop ROI on GeoTiff Maps (DOM & DSM) and Point Cloud (`ROI Cropper`).
+3. Save cropped results to corresponding files (`ROI Saver`).
+
+This project tried to use packges based on pure-python, instead of installing some heavy packages (Open3D, OpenCV) and hard to install packages (GDAL dependices) for one or two individual functions. This may cause efficiency loss and differences in coding habit.
+
+<p align="center">
+  <img alt="GitHub Downloads" height="400px" src="https://api.star-history.com/svg?repos=UTokyo-FieldPhenomics-Lab/EasyIDP&type=Date">
+</p>
+
+## <div align="center">Documentation</div>
+
+Please check [Official Documents](https://easyidp.readthedocs.io/en/latest/) ( [中文](https://easyidp.readthedocs.io/zh_CN/latest/) | [日本語(翻訳募集)](https://easyidp.readthedocs.io/ja/latest/) ) for full documentations. And please also use the [Github Discussion](https://github.com/UTokyo-FieldPhenomics-Lab/EasyIDP/discussions) when you meet any problems.
+
+## <div align="center">References</div>
+
+Please cite this paper if this project helps you：
+
+```latex
+@Article{wang_easyidp_2021,
+AUTHOR = {Wang, Haozhou and Duan, Yulin and Shi, Yun and Kato, Yoichiro and Ninomiya, Seish and Guo, Wei},
+TITLE = {EasyIDP: A Python Package for Intermediate Data Processing in UAV-Based Plant Phenotyping},
+JOURNAL = {Remote Sensing},
+VOLUME = {13},
+YEAR = {2021},
+NUMBER = {13},
+ARTICLE-NUMBER = {2622},
+URL = {https://www.mdpi.com/2072-4292/13/13/2622},
+ISSN = {2072-4292},
+DOI = {10.3390/rs13132622}
+}
+```
+
+We also thanks the benefits from the following open source projects:
+
+* package main (**for users**)
+  * numpy: [https://numpy.org/](https://numpy.org/)
+  * matplotlib:[https://matplotlib.org/](https://matplotlib.org/)
+  * scikit-image: [https://github.com/scikit-image/scikit-image](https://github.com/scikit-image/scikit-image)
+  * pyproj: [https://github.com/pyproj4/pyproj](https://github.com/pyproj4/pyproj)
+  * tifffile: [https://github.com/cgohlke/tifffile](https://github.com/cgohlke/tifffile)
+  * imagecodecs: [https://github.com/cgohlke/imagecodecs](https://github.com/cgohlke/imagecodecs)
+  * shapely: [https://github.com/shapely/shapely](https://github.com/shapely/shapely)
+  * laspy/lasrs/lasio: [https://github.com/laspy/laspy](https://github.com/laspy/laspy)
+  * geojson: [https://github.com/jazzband/geojson](https://github.com/jazzband/geojson)
+  * plyfile: [https://github.com/dranjan/python-plyfile](https://github.com/dranjan/python-plyfile)
+  * pyshp: [https://github.com/GeospatialPython/pyshp](https://github.com/GeospatialPython/pyshp)
+  * tabulate: [https://github.com/astanin/python-tabulate](https://github.com/astanin/python-tabulate)
+  * tqdm: [https://github.com/tqdm/tqdm](https://github.com/tqdm/tqdm)
+  * gdown: [https://github.com/wkentaro/gdown](https://github.com/wkentaro/gdown)
+* package documentation (**for developers**)
+  * sphinx: [https://github.com/sphinx-doc/sphinx](https://github.com/sphinx-doc/sphinx)
+  * nbsphinx: [https://github.com/spatialaudio/nbsphinx](https://github.com/spatialaudio/nbsphinx)
+  * sphinx-gallery: [https://github.com/sphinx-gallery/sphinx-gallery](https://github.com/sphinx-gallery/sphinx-gallery)
+  * sphinx-inline-tabs: [https://github.com/pradyunsg/sphinx-inline-tabs](https://github.com/pradyunsg/sphinx-inline-tabs)
+  * sphinx-intl: [https://github.com/sphinx-doc/sphinx-intl](https://github.com/sphinx-doc/sphinx-intl)
+  * sphinx-rtc-theme: [https://github.com/readthedocs/sphinx_rtd_theme](https://github.com/readthedocs/sphinx_rtd_theme)
+  * furo: [https://github.com/pradyunsg/furo](https://github.com/pradyunsg/furo)
+* package testing and releasing (**for developers**)
+  * pytest: [https://github.com/pytest-dev/pytest](https://github.com/pytest-dev/pytest)
+  * packaging: [https://github.com/pypa/packaging](https://github.com/pypa/packaging)
+  * wheel: [https://github.com/pypa/wheel](https://github.com/pypa/wheel)
+
+This project was partially funded by:
+
+* the JST AIP Acceleration Research “Studies of CPS platform to raise big-data-driven AI agriculture”; 
+* the SICORP Program JPMJSC16H2; 
+* CREST Programs JPMJCR16O2 and JPMJCR16O1; 
+* the International Science & Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAASTIP); 
+* the National Natural Science Foundation of China U19A2061.