hoa-tools 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

hoa_tools/data/metadata/metadata/S-22-16_brain_complete-organ_19.59um_bm18.json

@@ -0,0 +1,266 @@
+{
+  "name": "S-22-16_brain_complete-organ_19.59um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [7642, 7642, 8969],
+    "voxel_size_um": 19.59,
+    "gcs_url": "zarr://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-22-16/brain/19.59um_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": "S-22-16",
+    "age": 73,
+    "sex": "M",
+    "weight": 177.0,
+    "height": 89.0,
+    "cause_of_death": null,
+    "date_of_death": null,
+    "medical_history": "hemorrhagic shock, GI bleeding and aspiration, duodenal ulcers with bleeding Forrest Ib, ulcus excision, COVID19 Jan 2022, hypertension,Brain: transient ischemic attack of the left medial artery (ACM), arachnoidal cysts in the temporal lobe",
+    "diabetes": "Type 2",
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2022-07-09",
+    "beamline": "BM18",
+    "energy": 90.0,
+    "current_start": 196.99,
+    "filling_mode": null,
+    "n_frames": 9900,
+    "n_ref": 3,
+    "n_dark": 100,
+    "latency_time": 0.0012,
+    "exposure_time": 0.012,
+    "subframe_time": null,
+    "n_subframes": 3,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "quarter",
+    "z_step": null,
+    "scan_time": 402.0,
+    "filters": ["Sapphire 5mm", "SiO2 30mm block"],
+    "scintillator": "LuAG:Ce 2000um, reflective",
+    "optic": "DZoom",
+    "optic_magnification": 0.273,
+    "distance_source_sample": null,
+    "distance_sample_detector": 15000.0,
+    "sensor_name": null,
+    "sensor_mode": null,
+    "sensor_roi_x_size": 3948,
+    "sensor_roi_y_size": 432,
+    "sensor_binning": null,
+    "pixel_size": 19.59,
+    "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 19.59um of the brain of donor S-22-16, 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": "Camille",
+        "last_name": "Berruyer",
+        "orcid": "0000-0002-0046-2972",
+        "roles": ["Investigation"]
+      },
+      {
+        "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": "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": "Jingwen",
+        "last_name": "Liu",
+        "orcid": "0009-0009-8373-0079",
+        "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": "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",
+          "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": "Shahrokh",
+        "last_name": "Rahmani",
+        "orcid": "0000-0002-5773-7076",
+        "roles": ["Investigation"]
+      },
+      {
+        "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",
+      "Camille Berruyer",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Jingwen Liu",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Maximilian Ackermann",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Philippe Chaffanjon",
+      "Rebecca Shipley",
+      "Shahrokh Rahmani",
+      "Simon Walker-Samuel",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.1"
+}

hoa_tools/dataset.py

@@ -122,7 +122,7 @@ class Dataset(HOAMetadata):
         """
         Get a set of all datasets that are registered (even indirectly) to this dataset.
         """
-        import hoa_tools.registration
+        import hoa_tools.registration  # noqa: PLC0415
 
         dataset_names = nx.node_connected_component(
             hoa_tools.registration.Inventory._graph.to_undirected(),  # noqa: SLF001
@@ -242,7 +242,7 @@ def change_metadata_directory(data_dir: Path) -> None:
 
 
 def _populate_registrations_from_metadata(datasets: dict[str, Dataset]) -> None:
-    from hoa_tools.registration import Inventory, build_transform
+    from hoa_tools.registration import Inventory, build_transform  # noqa: PLC0415
 
     Inventory._clear()  # noqa: SLF001
     for dataset_name in datasets:
@@ -250,12 +250,18 @@ def _populate_registrations_from_metadata(datasets: dict[str, Dataset]) -> None:
         if (registration := dataset.registration) is not None:
             source_dataset = _DATASETS[registration.source_dataset]
             if registration.target_dataset not in _DATASETS:
-                warnings.warn(
-                    f"Did not find target dataset {registration.target_dataset} "
-                    f"in dataset inventory. Not adding {registration.source_dataset} "
-                    "to registration inventory.",
-                    stacklevel=1,
-                )
+                # Some datasets don't have their parent datasets release yet - only warn
+                # if we're expecting a parent dataset
+                if registration.source_dataset not in [
+                    "A129_lung_VOI-02_2.0um_bm18"
+                ] and not registration.source_dataset.startswith("LADAF-2021-17_brain"):
+                    warnings.warn(
+                        f"Did not find target dataset {registration.target_dataset} "
+                        f"in dataset inventory. "
+                        f"Not adding {registration.source_dataset} "
+                        "to registration inventory.",
+                        stacklevel=1,
+                    )
                 continue
             target_dataset = _DATASETS[registration.target_dataset]
             transform = build_transform(

hoa_tools/metadata.py

@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  metadata-schema.json
-#   timestamp: 2025-04-25T10:05:35+00:00
+#   timestamp: 2025-07-07T14:56:30+00:00
 
 from __future__ import annotations
 
@@ -486,6 +486,7 @@ class Scan(BaseModel):
             "uniform multibunch",
             "28*12+1 bunch",
             "4 bunch",
+            "2*1/3 multibunch",
         ]
         | None,
         Field(
@@ -604,6 +605,7 @@ class Scan(BaseModel):
             "GGG 20um",
             "GAGG 1000um, reflective",
             "GAGG 100um, reflective",
+            "GAGG 50um, reflective",
             "Dual LySO:Ce 5000um, reflective",
         ]
         | None,
@@ -762,6 +764,6 @@ class HOAMetadata(BaseModel):
     ] = None
     citation: Annotated[Citation, Field(title="Dataset citation")]
     metadata_version: Annotated[
-        Literal["1.0"],
+        Literal["1.1"],
         Field(description="Version of this metadata file.", title="Metadata Version"),
-    ] = "1.0"
+    ] = "1.1"

{hoa_tools-1.0.4.dist-info → hoa_tools-1.0.6.dist-info}/METADATA

@@ -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