hoa-tools 1.0.4__tar.gz → 1.0.6__tar.gz

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/.pre-commit-config.yaml

@@ -3,13 +3,13 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.12.3
     hooks:
       - id: ruff
       - id: ruff-format
 
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.5.3
+    rev: v3.6.2
     hooks:
       - id: prettier
 

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/.readthedocs.yml

@@ -5,9 +5,9 @@ submodules:
     - src/hoa_tools/data/metadata
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.13"
 
 python:
   install:

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0.4
+Version: 1.0.6
 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-1.0.4 → hoa_tools-1.0.6}/docs/tutorial/fetching_data.py

@@ -32,7 +32,7 @@ data_array
 # As an example, lets fetch and show a slice in the x-y plane::
 
 
-middle_slice = data_array.isel(z=437)
+middle_slice = data_array.isel(z=337)
 im = middle_slice.plot(cmap="Grays_r")
 im.axes.set_aspect("equal")
 

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/src/hoa_tools/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.4'
-__version_tuple__ = version_tuple = (1, 0, 4)
+__version__ = version = '1.0.6'
+__version_tuple__ = version_tuple = (1, 0, 6)

hoa_tools-1.0.6/src/hoa_tools/data/metadata/metadata/A129_lung_VOI-02_2.0um_bm18.json

@@ -0,0 +1,221 @@
+{
+  "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": "md1389",
+    "title": "HUB Proposal: Human Organ Atlas Hub (HOAHub)",
+    "proposers": [
+      "Peter Lee",
+      "Claire Walsh",
+      "Anastasia Yendiki",
+      "Maximilian Ackermann",
+      "Alexandre Bellier",
+      "Bernadette de Bakker",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Stijn Verleden"
+    ]
+  },
+  "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": "Anastasia",
+        "last_name": "Yendiki",
+        "orcid": "0000-0003-1386-3828",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Bernadette",
+        "last_name": "de Bakker",
+        "orcid": "0000-0003-0758-4064",
+        "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": "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": "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": "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": "Stijn",
+        "last_name": "Verleden",
+        "orcid": "0000-0002-9656-5844",
+        "roles": ["Funding acquisition", "Resources"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-2184066672",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Anastasia Yendiki",
+      "Bernadette de Bakker",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Joseph Jacob",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Stijn Verleden",
+      "Theresa Urban"
+    ]
+  },
+  "metadata_version": "1.1"
+}

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/src/hoa_tools/data/metadata/metadata/A186_lung_right_VOI-3_4.26um_bm18.json

@@ -77,7 +77,7 @@
       "Anastasia Yendiki",
       "Maximilian Ackermann",
       "Alexandre Bellier",
-      "Bernadette De Bakker",
+      "Bernadette de Bakker",
       "Paul Tafforeau",
       "Danny Jonigk",
       "Stijn Verleden"
@@ -108,7 +108,7 @@
       {
         "first_name": "Anastasia",
         "last_name": "Yendiki",
-        "orcid": null,
+        "orcid": "0000-0003-1386-3828",
         "roles": ["Funding acquisition"]
       },
       {
@@ -119,8 +119,8 @@
       },
       {
         "first_name": "Bernadette",
-        "last_name": "De Bakker",
-        "orcid": null,
+        "last_name": "de Bakker",
+        "orcid": "0000-0003-0758-4064",
         "roles": ["Funding acquisition"]
       },
       {
@@ -243,13 +243,13 @@
         "roles": ["Data curation", "Investigation", "Software"]
       }
     ],
-    "doi": null,
+    "doi": "10.15151/ESRF-DC-1992760497",
     "author_list": [
       "The Human Organ Atlas Collaboration",
       "Alexandre Bellier",
       "Anastasia Yendiki",
       "Andrew Keenlyside",
-      "Bernadette De Bakker",
+      "Bernadette de Bakker",
       "Birger Tielemans",
       "Claire Walsh",
       "Daisuke Yamada",
@@ -271,5 +271,5 @@
       "Theresa Urban"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

{hoa_tools-1.0.4 → hoa_tools-1.0.6}/src/hoa_tools/data/metadata/metadata/A186_lung_right_complete-organ_24.132um_bm18.json

@@ -77,7 +77,7 @@
       "Anastasia Yendiki",
       "Maximilian Ackermann",
       "Alexandre Bellier",
-      "Bernadette De Bakker",
+      "Bernadette de Bakker",
       "Paul Tafforeau",
       "Danny Jonigk",
       "Stijn Verleden"
@@ -102,7 +102,7 @@
       {
         "first_name": "Anastasia",
         "last_name": "Yendiki",
-        "orcid": null,
+        "orcid": "0000-0003-1386-3828",
         "roles": ["Funding acquisition"]
       },
       {
@@ -113,8 +113,8 @@
       },
       {
         "first_name": "Bernadette",
-        "last_name": "De Bakker",
-        "orcid": null,
+        "last_name": "de Bakker",
+        "orcid": "0000-0003-0758-4064",
         "roles": ["Funding acquisition"]
       },
       {
@@ -237,13 +237,13 @@
         "roles": ["Data curation", "Investigation", "Software"]
       }
     ],
-    "doi": null,
+    "doi": "10.15151/ESRF-DC-1997004305",
     "author_list": [
       "The Human Organ Atlas Collaboration",
       "Alexandre Bellier",
       "Anastasia Yendiki",
       "Andrew Keenlyside",
-      "Bernadette De Bakker",
+      "Bernadette de Bakker",
       "Birger Tielemans",
       "Claire Walsh",
       "Daisuke Yamada",
@@ -265,5 +265,5 @@
       "Theresa Urban"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }