Rhapso 0.1.99__py3-none-any.whl → 0.1.993__py3-none-any.whl

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Files changed (12) hide show
  1. Rhapso/matching/ransac_matching.py +32 -36
  2. Rhapso/pipelines/ray/aws/alignment_pipeline.py +17 -14
  3. Rhapso/pipelines/ray/interest_point_matching.py +9 -9
  4. Rhapso/pipelines/ray/local/alignment_pipeline.py +20 -17
  5. Rhapso/pipelines/ray/solver.py +7 -3
  6. Rhapso/solver/global_optimization.py +5 -5
  7. Rhapso/split_dataset/save_xml.py +490 -93
  8. {rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/METADATA +38 -26
  9. {rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/RECORD +12 -12
  10. {rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/WHEEL +0 -0
  11. {rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/licenses/LICENSE +0 -0
  12. {rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/top_level.txt +0 -0
{rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: Rhapso
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- Version: 0.1.99
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+ Version: 0.1.993
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  Summary: A python package for aligning and stitching light sheet fluorescence microscopy images
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  Author: ND
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  Author-email: sean.fite@alleninstitute.org
@@ -9,13 +9,9 @@ Project-URL: Roadmap, https://github.com/AllenNeuralDynamics/Rhapso/issues
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  Classifier: Development Status :: 3 - Alpha
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  Classifier: Intended Audience :: Developers
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  Classifier: Natural Language :: English
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3.7
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- Classifier: Programming Language :: Python :: 3.8
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- Classifier: Programming Language :: Python :: 3.9
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  Classifier: Programming Language :: Python :: 3.10
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  Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.7
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+ Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: pandas
@@ -33,6 +29,7 @@ Requires-Dist: matplotlib==3.10.0
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  Requires-Dist: memory-profiler==0.61.0
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  Requires-Dist: s3fs==2024.12.0
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  Requires-Dist: scikit-learn
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+ Requires-Dist: click==8.2.1
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  Dynamic: author
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  Dynamic: author-email
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  Dynamic: classifier
@@ -46,7 +43,7 @@ Dynamic: summary
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  # Rhapso
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- This is the code base for **Rhapso**, a modular Python toolkit for the alignment and stitching of large-scale microscopy datasets.
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+ This is the official code base for **Rhapso**, a modular Python toolkit for the alignment and stitching of large-scale microscopy datasets.
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  [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
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  [![Python Version](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/)
@@ -64,6 +61,8 @@ This is the code base for **Rhapso**, a modular Python toolkit for the alignment
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  - [Performance](#performance)
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  - [Layout](#layout)
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  - [Installation](#installation)
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+ - [How To Start](#how-to-start)
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+ - [Try Rhapso on Sample Data](#try-rhapso-on-sample-data)
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  - [Ray](#ray)
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  - [Run Locally w/ Ray](#run-locally-with-ray)
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  - [Run on AWS Cluster w/ Ray](#run-on-aws-cluster-with-ray)
@@ -88,13 +87,7 @@ Rhapso is still loading... and while we wrap up development, a couple things to
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  ## Summary
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  Rhapso is a set of Python components used to register, align, and stitch large-scale, overlapping, tile-based, multiscale microscopy datasets. Its stateless components can run on a single machine or scale out across cloud-based clusters.
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- Rhapso is published on PyPI and can be installed with:
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-
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- ```bash
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- pip install Rhapso
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- ```
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- <br>
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+ Rhapso is published on PyPI.
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  Rhapso was developed by the Allen Institute for Neural Dynamics.
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@@ -213,6 +206,24 @@ A good way to get started:
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  <br>
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+ ## Try Rhapso on Sample Data
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+ The quickest way to get familiar with Rhapso is to run it on a real dataset. We have a small (10GB) Z1 example hosted in a public S3 bucket, so you can access it without special permissions. It’s a good starting point to copy and adapt for your own alignment workflows.
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+ XML (input)
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+ - s3://aind-open-data/HCR_802704_2025-08-30_02-00-00_processed_2025-10-01_21-09-24/image_tile_alignment/single_channel_xmls/channel_488.xml
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+ Image prefix (referenced by the XML)
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+ - s3://aind-open-data/HCR_802704_2025-08-30_02-00-00_processed_2025-10-01_21-09-24/image_radial_correction/
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+ <br>
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+ **Note:** Occasionally we clean up our aind-open-data bucket. If you find this dataset does not exist, please create an issue and we will replace it.
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+
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+ ---
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+ <br>
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+
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  ## High Level Approach to Registration, Alignment, and Fusion
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  This process has a lot of knobs and variations, and when used correctly, can work for a broad range of datasets.
@@ -400,25 +411,26 @@ python Rhapso/pipelines/ray/aws/alignment_pipeline.py
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  | Parameter | Feature / step | What it does | Typical range |
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  | :---------------------------- | :------------------- | :---------------------------------------------------------------- | :------------- |
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  | `model_min_matches` | RANSAC | Minimum correspondences to estimate a rigid transform | 18 – 32 |
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- | `inlier_factor` | RANSAC | Inlier tolerance scaling; larger = looser inlier threshold | 30 – 100 |
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- | `lambda_value` | RANSAC | Regularization strength during model fitting | 0.1 – 0.05 |
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+ | `inlier_threshold` | RANSAC | Inlier tolerance scaling; larger = looser inlier threshold | 50 – 100 |
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+ | `min_inlier_ratio` | RANSAC | Regularization strength during model fitting | 0.1 – 0.05 |
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  | `num_iterations` | RANSAC | Number of RANSAC trials; higher = more robust, slower | 10,0000 |
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- | `regularization_weight` | RANSAC | Weight applied to the regularization term | 1.0 |
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+ | `regularization_weight` | RANSAC | Weight applied to the regularization term | 0.05 - 1.0 |
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  ```
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  <br>
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  ### Solver
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  ```
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- | Parameter | Feature / step | What it does | Typical range |
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- | :------------------- | :------------- | :----------------------------------------------------------------- | :------------------ |
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- | `relative_threshold` | Graph pruning | Reject edges with residuals above dataset-relative cutoff | 3.5 |
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- | `absolute_threshold` | Graph pruning | Reject edges above an absolute error bound (detection-space units) | 7.0 |
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- | `min_matches` | Graph pruning | Minimum matches required to retain an edge between tiles | 3 |
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- | `damp` | Optimization | Damping for iterative solver; higher can stabilize tough cases | 1.0 |
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- | `max_iterations` | Optimization | Upper bound on solver iterations | 10,0000 |
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- | `max_allowed_error` | Optimization | Overall error cap; `inf` disables hard stop by error | `inf` |
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- | `max_plateauwidth` | Early stopping | Stagnation window before stopping on no improvement | 200 |
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+ | Parameter | Feature / step | What it does | Typical range |
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+ | :----------------------- | :------------- | :----------------------------------------------------------------- | :------------------ |
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+ | `relative_threshold` | Graph pruning | Reject edges with residuals above dataset-relative cutoff | 3.5 |
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+ | `absolute_threshold` | Graph pruning | Reject edges above an absolute error bound (detection-space units) | 7.0 |
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+ | `min_matches` | Graph pruning | Minimum matches required to retain an edge between tiles | 3 |
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+ | `damp` | Optimization | Damping for iterative solver; higher can stabilize tough cases | 1.0 |
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+ | `max_iterations` | Optimization | Upper bound on solver iterations | 10,0000 |
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+ | `max_allowed_error` | Optimization | Overall error cap; `inf` disables hard stop by error | `inf` |
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+ | `max_plateauwidth` | Early stopping | Stagnation window before stopping on no improvement | 200 |
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+ | `regularization_weight` | RANSAC | Weight applied to the regularization term | 0.05 - 1.0 |
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  ```
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{rhapso-0.1.99.dist-info → rhapso-0.1.993.dist-info}/RECORD RENAMED
@@ -56,29 +56,29 @@ Rhapso/fusion/neuroglancer_link_gen/utils/transfer.py,sha256=8hFBM8lmCV3TsEEVXZk
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  Rhapso/fusion/neuroglancer_link_gen/utils/utils.py,sha256=Q0jKPGI39ScCHDgVEoWbrZrBrEluCjm69z28T3JScTc,7322
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  Rhapso/matching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/matching/load_and_transform_points.py,sha256=UEV9gnWyl2z4zAUR2Z_ewX1_TWoS-IpXPL-qRB1_Ms8,16416
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- Rhapso/matching/ransac_matching.py,sha256=PH9JpWqCrWcZoDvwG_Zs2FSk2cCdIX9be_6y2ix-3RI,20031
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+ Rhapso/matching/ransac_matching.py,sha256=BWSRmckG2GiA49RuGnja4le-Xo5o9aY53Yawes9P-_E,20268
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  Rhapso/matching/save_matches.py,sha256=OYHzzGoF9-PTVfQZBJ7HaJ9JYB_Q8ZazH-f3HljxzLQ,4720
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  Rhapso/matching/xml_parser.py,sha256=nP_jA_jEfAFPzt6Al91NpwWEk-Klk8P5QzNINJYVksU,11527
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  Rhapso/pipelines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/pipelines/ray/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/pipelines/ray/evaluation.py,sha256=k05e72WKu9UkptJkjk_rkScjn1zGOhIG1rTOLkxkOLI,2610
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  Rhapso/pipelines/ray/interest_point_detection.py,sha256=NZ2Egm81KPC1dFncz_6srW0TYhBTpKqy80nEk0DigEU,6595
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- Rhapso/pipelines/ray/interest_point_matching.py,sha256=aM-83D3JJUrkiWT0hogpcyxUw7h78kKegYtUFKMQu3s,5697
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+ Rhapso/pipelines/ray/interest_point_matching.py,sha256=0wdCxcz-PeNSrxLIZpHpUyJLOvp7tM8S6LH2k1t2woA,5746
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  Rhapso/pipelines/ray/matching_stats.py,sha256=7NZ4rQPTKMwzJBrPXkVbiWkzIeH4h9PfDozqrUo8TKU,4199
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- Rhapso/pipelines/ray/solver.py,sha256=JqNZPyd_0tliM3mu8voDNcQuhkgwMKF5fBMzfjVMCy8,6198
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+ Rhapso/pipelines/ray/solver.py,sha256=FK02ttFOvVRHTvlsBJ_kJ4GdwLHfIa3ljZ6VhE8FxS0,6458
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  Rhapso/pipelines/ray/split_dataset.py,sha256=JVMd3qYw17Em-rQDvufSAaqaPWw5kf9yWpf5ShSh97M,2943
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  Rhapso/pipelines/ray/aws/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- Rhapso/pipelines/ray/aws/alignment_pipeline.py,sha256=JvSB08mIskgqzc-U-6vOprl5k7i9UN5yOgDOKtimIJ0,9716
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+ Rhapso/pipelines/ray/aws/alignment_pipeline.py,sha256=c_UUw_90xnoAJ5zYuU5OD0Uzr1cPOqsZ6aXHOQauYCI,10015
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  Rhapso/pipelines/ray/aws/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/pipelines/ray/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- Rhapso/pipelines/ray/local/alignment_pipeline.py,sha256=OFdns9kILtAQD8KNU7MoLXQeZba1q4YV9LiLVSo8fi0,6712
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+ Rhapso/pipelines/ray/local/alignment_pipeline.py,sha256=EV2e0Kfx7uSHaIVMTKId-NG8f6B4TCWnI5yqSRrmuFE,6989
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  Rhapso/pipelines/ray/param/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/solver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/solver/compute_tiles.py,sha256=-7QFrZZfh1iW1nDdlBORlcqOGf7urJmgjWOj6DfDdHQ,20471
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  Rhapso/solver/concatenate_models.py,sha256=-763cwYyyHM6b7E5RkHMRtykFrVjeVeB1l0jFeoLfnI,4472
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  Rhapso/solver/connected_graphs.py,sha256=wKxOOKRNd4MctYRX677hiFIYHLAg3GinkpqDqO0ad50,3603
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  Rhapso/solver/data_prep.py,sha256=nS96_4MJ0TcHyFMsGDS82n0R-aUm8J99g8d_MrWpsik,7753
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- Rhapso/solver/global_optimization.py,sha256=6qYXHmJRCTf-4gSwFgmy9IBUBUp7SuL1kMOER8cTx6A,13614
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+ Rhapso/solver/global_optimization.py,sha256=Yl9_GlZDVLHtYtmlRY7qS0CX7c3c4zYxexIaGJVtsGY,13720
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  Rhapso/solver/model_and_tile_setup.py,sha256=WqCK9_sSMJ5MFmvIYi1_x1Sx_9giYORpCfcirZsMNOI,4889
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  Rhapso/solver/pre_align_tiles.py,sha256=BccXMr5cZILM8U0ZzhUyflQYx_WUQzvNDdX-S_u4Roo,11100
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  Rhapso/solver/save_results.py,sha256=dIkQ3SiGNlKx5z-6k_o_O4WjANxKYLJQ059URnuxVJw,3985
@@ -87,15 +87,15 @@ Rhapso/solver/xml_to_dataframe_solver.py,sha256=u96DPnZNDa-TgimsPqyZlIvHk4A1e8yZ
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  Rhapso/split_dataset/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  Rhapso/split_dataset/compute_grid_rules.py,sha256=dCAuNs4D7SaCfTXp54lchgttZVSgLH5f1tQWtkwr_ws,3028
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  Rhapso/split_dataset/save_points.py,sha256=k-jH-slmxkbrxDl-uJvDkwOedi6cg7md3kg_a0NdL24,3713
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- Rhapso/split_dataset/save_xml.py,sha256=Iq1UdFa8sdnWGygfIpDi4F5In-SCWggpl7lnuDTxkHE,14280
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+ Rhapso/split_dataset/save_xml.py,sha256=55NdzfHPGAhpR1QYaDwXPZQlZlP6T9fymhJaOwTuZh0,29561
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  Rhapso/split_dataset/split_images.py,sha256=2RzAi0btV1tmh4le9QotRif1IYUU6_4pLcGGpFBM9zk,22434
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  Rhapso/split_dataset/xml_to_dataframe_split.py,sha256=ByaLzJ4sqT417UiCQU31_CS_V4Jms7pjMbBl0ZdSNNA,8570
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- rhapso-0.1.99.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
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+ rhapso-0.1.993.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
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  tests/__init__.py,sha256=LYf6ZGyYRcduFFSaOLmnw3rTyfS3XLib0dsTHDWH0jo,37
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  tests/test_detection.py,sha256=NtFYR_du9cbKrclQcNiJYsKzyqly6ivF61pw6_NICcM,440
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  tests/test_matching.py,sha256=QX0ekSdyIkPpAsXHfSMqJUUlNZg09caSlhhUM63MduM,697
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  tests/test_solving.py,sha256=t8I9XPV_4ZFM-DJpgvdYXxkG2_4DQgqs-FFyE5w8Nfg,695
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- rhapso-0.1.99.dist-info/METADATA,sha256=kqyfZB6PEVsMDtjj-8QH_P1VxJvAQxMG4wUdmvVXeYY,18488
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- rhapso-0.1.99.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
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- rhapso-0.1.99.dist-info/top_level.txt,sha256=NXvsrsTfdowWbM7MxEjkDZE2Jo74lmq7ruWkp70JjSw,13
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- rhapso-0.1.99.dist-info/RECORD,,
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+ rhapso-0.1.993.dist-info/METADATA,sha256=U_wnul9wYKBsJqbjbs2FluO8uiAbaFTqm5ntyUxfzps,19298
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+ rhapso-0.1.993.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
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+ rhapso-0.1.993.dist-info/top_level.txt,sha256=NXvsrsTfdowWbM7MxEjkDZE2Jo74lmq7ruWkp70JjSw,13
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+ rhapso-0.1.993.dist-info/RECORD,,