hoa-tools 1.0.7__tar.gz → 1.0.8__tar.gz

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/.github/workflows/publish.yml

@@ -8,13 +8,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
           submodules: true
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 
@@ -45,7 +45,7 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: python-package-distributions
           path: dist/

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/.github/workflows/tests.yml

@@ -19,7 +19,7 @@ jobs:
           - "3.13"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
@@ -49,7 +49,7 @@ jobs:
           - "3.12"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.3
+    rev: v0.12.4
     hooks:
       - id: ruff
       - id: ruff-format

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0.7
+Version: 1.0.8
 Summary: Tools for working with the Human Organ Atlas
 Author-email: David Stansby <d.stansby@ucl.ac.uk>
 License: Copyright (c) 2024, David Stansby

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/src/hoa_tools/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '1.0.7'
-__version_tuple__ = version_tuple = (1, 0, 7)
+__version__ = version = '1.0.8'
+__version_tuple__ = version_tuple = (1, 0, 8)
+
+__commit_id__ = commit_id = 'g0f5407271'

hoa_tools-1.0.8/src/hoa_tools/data/metadata/metadata/A129_lung_VOI-02_2.0um_bm18.json

@@ -0,0 +1,286 @@
+{
+  "name": "A129_lung_VOI-02_2.0um_bm18",
+  "dataset_type": "zoom",
+  "voi": "VOI-02",
+  "data": {
+    "shape": [7102, 7102, 15491],
+    "voxel_size_um": 2.0,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/A129/lung/2.0um_VOI-02_bm18/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": null,
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": null,
+    "stabilisation_medium": null,
+    "degassing_method": null,
+    "scan_solvent": null,
+    "scan_solvent_concentration": null,
+    "scan_temperature": "room temperature"
+  },
+  "donor": {
+    "id": "A129",
+    "age": 30,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": "not applicable - transplant organ",
+    "date_of_death": null,
+    "medical_history": "transplant-yes, explant: PPFE",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2023-11-04",
+    "beamline": "BM18",
+    "energy": 84.0,
+    "current_start": 198.36135,
+    "filling_mode": "uniform multibunch",
+    "n_frames": 12000,
+    "n_ref": 101,
+    "n_dark": 3,
+    "latency_time": 0.0075,
+    "exposure_time": 0.075,
+    "subframe_time": 0.075,
+    "n_subframes": 1,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 6,
+    "acquisition": "half",
+    "z_step": 5.0,
+    "scan_time": 992.728934,
+    "filters": ["Sapphire 1mm", "Mo 0.23mm", "Psho 10mm"],
+    "scintillator": "LuAG:Ce 250um",
+    "optic": "Zoom",
+    "optic_magnification": 2.101245043596107,
+    "distance_source_sample": 177450.0,
+    "distance_sample_detector": 2000.0,
+    "sensor_name": "Iris15",
+    "sensor_mode": null,
+    "sensor_roi_x_size": 5056,
+    "sensor_roi_y_size": 2960,
+    "sensor_binning": [1, 1],
+    "pixel_size": 2.0,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1290",
+    "title": "Bridging the gap between cellular and whole body imaging using Hierarchical Phase-Contrast Tomography: HiP-CT",
+    "proposers": [
+      "Peter Lee",
+      "Claire Walsh",
+      "Brian Bay",
+      "Elodie Boller",
+      "Maximilian Ackermann",
+      "Alexandre Bellier",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Simon Walker-Samuel",
+      "Philippe Chaffanjon",
+      "Danny Jonigk",
+      "Willi Wagner",
+      "Rebecca Shipley"
+    ]
+  },
+  "registration": {
+    "source_dataset": "A129_lung_VOI-02_2.0um_bm18",
+    "target_dataset": "A129_lung_complete-organ_20.01um_bm18",
+    "translation": [1509.2014617251673, 492.7553509572563, 2478.7641987064226],
+    "rotation": 0.10001492736704592,
+    "scale": 0.0999497605784577
+  },
+  "citation": {
+    "title": "Zoom (VOI-02) at 2.0um of the lung of donor A129, scanned at ESRF on beamline BM18.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "first_name": "Alexandre",
+        "last_name": "Bellier",
+        "orcid": "0000-0003-0907-0315",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Brian",
+        "last_name": "Bay",
+        "orcid": "0000-0002-6870-259X",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Claire",
+        "last_name": "Walsh",
+        "orcid": "0000-0003-3769-3392",
+        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Danny",
+        "last_name": "Jonigk",
+        "orcid": "0000-0002-5251-2281",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "David",
+        "last_name": "Stansby",
+        "orcid": "0000-0002-1365-1908",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Elodie",
+        "last_name": "Boller",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Eunjue",
+        "last_name": "Yi",
+        "orcid": null,
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Guillaume",
+        "last_name": "Gaisne",
+        "orcid": "0000-0002-3401-7930",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Hector",
+        "last_name": "Dejea I Velardo",
+        "orcid": "0000-0003-2584-9812",
+        "roles": ["Data curation", "Investigation"]
+      },
+      {
+        "first_name": "Jishizhan",
+        "last_name": "Chen",
+        "orcid": "0000-0002-1784-319X",
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Joanna",
+        "last_name": "Purzycka",
+        "orcid": "0000-0001-8742-5279",
+        "roles": ["Data curation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Jacob",
+        "orcid": "0000-0002-8054-2293",
+        "roles": ["Resources"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "roles": ["Funding acquisition", "Resources"]
+      },
+      {
+        "first_name": "Olivier",
+        "last_name": "Palombi",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Paul",
+        "last_name": "Tafforeau",
+        "orcid": "0000-0002-5962-1683",
+        "roles": [
+          "Conceptualization",
+          "Data curation",
+          "Funding acquisition",
+          "Investigation"
+        ]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Philippe",
+        "last_name": "Chaffanjon",
+        "orcid": "0000-0002-7954-2798",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Rebecca",
+        "last_name": "Shipley",
+        "orcid": "0000-0002-2818-6228",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Ryoko",
+        "last_name": "Egashira",
+        "orcid": "0000-0001-7566-546X",
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Simon",
+        "last_name": "Walker-Samuel",
+        "orcid": "0000-0003-3530-9166",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Stijn",
+        "last_name": "Verleden",
+        "orcid": "0000-0002-9656-5844",
+        "roles": ["Resources"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Willi",
+        "last_name": "Wagner",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-2184066672",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Brian Bay",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Eunjue Yi",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Jishizhan Chen",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Joseph Jacob",
+      "Maximilian Ackermann",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Philippe Chaffanjon",
+      "Rebecca Shipley",
+      "Ryoko Egashira",
+      "Simon Walker-Samuel",
+      "Stijn Verleden",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.1"
+}

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/src/hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_hippocampus_2.45um_bm05.json

@@ -81,13 +81,7 @@
       "Willi Wagner"
     ]
   },
-  "registration": {
-    "source_dataset": "LADAF-2020-31_brain_hippocampus_2.45um_bm05",
-    "target_dataset": "LADAF-2020-31_brain_complete-organ_25.08um_bm05",
-    "translation": [3744.647212922214, 1801.1225090914268, 2711.0471941068986],
-    "rotation": 0.20008306913931156,
-    "scale": 0.09768735671581703
-  },
+  "registration": null,
   "citation": {
     "title": "Zoom (hippocampus) at 2.45um of the brain of donor LADAF-2020-31, scanned at ESRF on beamline BM05.",
     "contributors": [

{hoa_tools-1.0.7 → hoa_tools-1.0.8}/src/hoa_tools/data/metadata/metadata/LADAF-2021-17_brain_VOI-03.2_2.256um_bm18.json

@@ -87,7 +87,13 @@
       "Rebecca Shipley"
     ]
   },
-  "registration": null,
+  "registration": {
+    "source_dataset": "LADAF-2021-17_brain_VOI-03.2_2.256um_bm18",
+    "target_dataset": "LADAF-2021-17_brain_complete-organ_7.72um_bm18",
+    "translation": [4263.227265344232, 4331.55200984121, 61.06221773571507],
+    "rotation": -34.29786969900008,
+    "scale": 0.29222907370962964
+  },
   "citation": {
     "title": "Zoom (VOI-03.2) at 2.256um of the brain of donor LADAF-2021-17, scanned at ESRF on beamline BM18.",
     "contributors": [

hoa_tools-1.0.8/src/hoa_tools/data/metadata/metadata/LADAF-2021-17_brain_complete-organ_7.72um_bm18.json

@@ -0,0 +1,240 @@
+{
+  "name": "LADAF-2021-17_brain_complete-organ_7.72um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [18709, 18709, 21517],
+    "voxel_size_um": 7.72,
+    "gcs_url": "zarr://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/brain/7.72um_complete-organ_bm18.ome.zarr/"
+  },
+  "sample": {
+    "organ": "brain",
+    "organ_context": null,
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": null,
+    "stabilisation_medium": null,
+    "degassing_method": null,
+    "scan_solvent": null,
+    "scan_solvent_concentration": null,
+    "scan_temperature": "room temperature"
+  },
+  "donor": {
+    "id": "LADAF-2021-17",
+    "age": 63,
+    "sex": "M",
+    "weight": 60.0,
+    "height": 178.0,
+    "cause_of_death": "Pancreatic cancer",
+    "date_of_death": "2020-03-27",
+    "medical_history": "stomach hypertrophy noticed during autopsy, stomach liquid into the lungs",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2022-08-17",
+    "beamline": "BM18",
+    "energy": 111.0,
+    "current_start": null,
+    "filling_mode": null,
+    "n_frames": 30000,
+    "n_ref": 10,
+    "n_dark": 3,
+    "latency_time": null,
+    "exposure_time": 0.03,
+    "subframe_time": null,
+    "n_subframes": null,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 33,
+    "acquisition": "quarter",
+    "z_step": null,
+    "scan_time": null,
+    "filters": null,
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 10000.0,
+    "sensor_name": null,
+    "sensor_mode": null,
+    "sensor_roi_x_size": 9599,
+    "sensor_roi_y_size": 21517,
+    "sensor_binning": null,
+    "pixel_size": 7.72,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1290",
+    "title": "Bridging the gap between cellular and whole body imaging using Hierarchical Phase-Contrast Tomography: HiP-CT",
+    "proposers": [
+      "Peter Lee",
+      "Claire Walsh",
+      "Brian Bay",
+      "Elodie Boller",
+      "Maximilian Ackermann",
+      "Alexandre Bellier",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Simon Walker-Samuel",
+      "Philippe Chaffanjon",
+      "Danny Jonigk",
+      "Willi Wagner",
+      "Rebecca Shipley"
+    ]
+  },
+  "registration": null,
+  "citation": {
+    "title": "Overview at 7.72um of the brain of donor LADAF-2021-17, scanned at ESRF on beamline BM18.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "first_name": "Alexandre",
+        "last_name": "Bellier",
+        "orcid": "0000-0003-0907-0315",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Brian",
+        "last_name": "Bay",
+        "orcid": "0000-0002-6870-259X",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Claire",
+        "last_name": "Walsh",
+        "orcid": "0000-0003-3769-3392",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "first_name": "Danny",
+        "last_name": "Jonigk",
+        "orcid": "0000-0002-5251-2281",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "David",
+        "last_name": "Stansby",
+        "orcid": "0000-0002-1365-1908",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Elodie",
+        "last_name": "Boller",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Guillaume",
+        "last_name": "Gaisne",
+        "orcid": "0000-0002-3401-7930",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Hector",
+        "last_name": "Dejea I Velardo",
+        "orcid": "0000-0003-2584-9812",
+        "roles": ["Data curation", "Investigation"]
+      },
+      {
+        "first_name": "Joanna",
+        "last_name": "Purzycka",
+        "orcid": "0000-0001-8742-5279",
+        "roles": ["Data curation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Olivier",
+        "last_name": "Palombi",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Paul",
+        "last_name": "Tafforeau",
+        "orcid": "0000-0002-5962-1683",
+        "roles": ["Conceptualization", "Data curation", "Funding acquisition"]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "first_name": "Philippe",
+        "last_name": "Chaffanjon",
+        "orcid": "0000-0002-7954-2798",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Rebecca",
+        "last_name": "Shipley",
+        "orcid": "0000-0002-2818-6228",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Simon",
+        "last_name": "Walker-Samuel",
+        "orcid": "0000-0003-3530-9166",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Willi",
+        "last_name": "Wagner",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      }
+    ],
+    "doi": null,
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Brian Bay",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Maximilian Ackermann",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Philippe Chaffanjon",
+      "Rebecca Shipley",
+      "Simon Walker-Samuel",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.1"
+}