hoa-tools 1.0.1__py3-none-any.whl → 1.0.2__py3-none-any.whl

hoa_tools/data/metadata/metadata/S-20-29_lung_left_VOI-05_6.5um_bm05.json

@@ -0,0 +1,205 @@
+{
+  "name": "S-20-29_lung_left_VOI-05_6.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-05",
+  "data": {
+    "shape": [3833, 3833, 20077],
+    "voxel_size_um": 6.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/lung-left/6.5um_VOI-05_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left",
+    "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-20-29",
+    "age": 80,
+    "sex": "M",
+    "weight": 170.0,
+    "height": 90.0,
+    "cause_of_death": "Acute right heart failure with extensive Pulmonary artery thrombembolism, diffuse alveolar damage, shock kidneys bilateral with acute kidney failure, and acute liver failure COVID-19 disease",
+    "date_of_death": null,
+    "medical_history": "Kidney failure, arterial hypertension, Z.n. Spondylodesis LWK 2 and sacral vertebra 2, SARS-CoV2 infection, symptoms of memory loss and predementia, Dandy-Walker syndrome variant, post-mortem diagnostic.",
+    "diabetes": "Type 2",
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-11-07",
+    "beamline": "BM05",
+    "energy": 95.0,
+    "current_start": 192.033,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0015,
+    "exposure_time": 0.015,
+    "subframe_time": null,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 59,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": 420.0,
+    "filters": ["Mo 0.1mm", "SiO2 50mm rods 10x5mm"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "Zoom",
+    "optic_magnification": 0.941,
+    "distance_source_sample": null,
+    "distance_sample_detector": 500.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 2043,
+    "sensor_roi_y_size": 20077,
+    "sensor_binning": null,
+    "pixel_size": 6.5,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1252",
+    "title": "Multiscale Quantification of Covid-19's impact on lung vasculature from whole lobe to alveolar/microvascular scales",
+    "proposers": [
+      "Peter Lee",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Maximilian Ackermann",
+      "Mark P. Kuhnel",
+      "Elodie Boller",
+      "Willi Wagner"
+    ]
+  },
+  "registration": {
+    "source_dataset": "S-20-29_lung_left_VOI-05_6.5um_bm05",
+    "target_dataset": "S-20-29_lung_left_complete-organ_25.31um_bm05",
+    "translation": [1257.7257673685622, 1005.485226013251, 789.8548884643609],
+    "rotation": -5.299835000447964,
+    "scale": 0.2568154947103331
+  },
+  "citation": {
+    "title": "Zoom (VOI-05) at 6.5um of the lung of donor S-20-29, scanned at ESRF on beamline BM05.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "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": "Mark",
+        "last_name": "P. Kuhnel",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "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": "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-1773964041",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Mark P. Kuhnel",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.0"
+}

hoa_tools/data/metadata/metadata/S-20-29_lung_left_complete-organ_25.31um_bm05.json

@@ -0,0 +1,199 @@
+{
+  "name": "S-20-29_lung_left_complete-organ_25.31um_bm05",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [3814, 5350, 6391],
+    "voxel_size_um": 25.31,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/lung-left/25.31um_complete-organ_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left",
+    "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-20-29",
+    "age": 80,
+    "sex": "M",
+    "weight": 170.0,
+    "height": 90.0,
+    "cause_of_death": "Acute right heart failure with extensive Pulmonary artery thrombembolism, diffuse alveolar damage, shock kidneys bilateral with acute kidney failure, and acute liver failure COVID-19 disease",
+    "date_of_death": null,
+    "medical_history": "Kidney failure, arterial hypertension, Z.n. Spondylodesis LWK 2 and sacral vertebra 2, SARS-CoV2 infection, symptoms of memory loss and predementia, Dandy-Walker syndrome variant, post-mortem diagnostic.",
+    "diabetes": "Type 2",
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-10-27",
+    "beamline": "BM05",
+    "energy": 96.0,
+    "current_start": 190.786,
+    "filling_mode": null,
+    "n_frames": 9990,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0007,
+    "exposure_time": 0.007,
+    "subframe_time": null,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "quarter",
+    "z_step": null,
+    "scan_time": 330.0,
+    "filters": ["Mo 0.1mm", "SiO2 50mm rods 10x5mm"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "Zoom",
+    "optic_magnification": 2.154,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3650.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": null,
+    "sensor_roi_y_size": null,
+    "sensor_binning": null,
+    "pixel_size": 25.31,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1252",
+    "title": "Multiscale Quantification of Covid-19's impact on lung vasculature from whole lobe to alveolar/microvascular scales",
+    "proposers": [
+      "Peter Lee",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Maximilian Ackermann",
+      "Mark P. Kuhnel",
+      "Elodie Boller",
+      "Willi Wagner"
+    ]
+  },
+  "registration": null,
+  "citation": {
+    "title": "Overview at 25.31um of the lung of donor S-20-29, scanned at ESRF on beamline BM05.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "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": "Mark",
+        "last_name": "P. Kuhnel",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "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": "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-1773966447",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Mark P. Kuhnel",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.0"
+}

hoa_tools/dataset.py

@@ -10,6 +10,7 @@ To get a [`Dataset`][hoa_tools.dataset.Dataset], use the
 [`get_dataset`][hoa_tools.dataset.get_dataset] function in this module.
 """
 
+import warnings
 from functools import cached_property
 from pathlib import Path
 from typing import Literal
@@ -24,10 +25,14 @@ import zarr.storage
 
 from hoa_tools._n5 import N5FSStore
 from hoa_tools.metadata import HOAMetadata
+from hoa_tools.types import PhysicalCoordinate
 
 __all__ = ["Dataset", "get_dataset"]
 
 
+_DATASETS: dict[str, "Dataset"]
+
+
 class Dataset(HOAMetadata):
     """
     An individual Human Organ Atlas dataset.
@@ -185,25 +190,19 @@ class Dataset(HOAMetadata):
         )
 
 
-def _get_datasets(data_dir: Path) -> dict[str, Dataset]:
+def _load_datasets_from_files(data_dir: Path) -> dict[str, Dataset]:
     """
     Load dataset metadtata files.
     """
-    return {
+    datasets = {
         f.stem: Dataset.model_validate_json(f.read_text())
         for f in (data_dir).glob("*.json")
     }
-
-
-_META_DIR = Path(__file__).parent / "data" / "metadata" / "metadata"
-_DATASETS = _get_datasets(_META_DIR)
-if len(_DATASETS) == 0:
-    raise ImportError(
-        "Did not find any dataset metadata files. "
-        "This means there is something wrong with the hoa-tools installation. "
-        "If you are installing from source, you might need to "
-        "initialise and fetch git submodules. "
-    )
+    if len(datasets) == 0:
+        raise FileNotFoundError(
+            f"Did not find any dataset metadata files at {data_dir}"  # noqa: EM102
+        )
+    return datasets
 
 
 def get_dataset(name: str) -> Dataset:
@@ -222,8 +221,53 @@ def change_metadata_directory(data_dir: Path) -> None:
     Designed for internal project members to load metadata files that aren't yet public.
     """
     global _DATASETS  # noqa: PLW0603
-    _DATASETS = _get_datasets(data_dir)
-    if len(_DATASETS) == 0:
-        raise FileNotFoundError(
-            f"Did not find any dataset metadata files at {data_dir}"  # noqa: EM102
-        )
+    _DATASETS = _load_datasets_from_files(data_dir)
+    _populate_registrations_from_metadata(_DATASETS)
+
+
+def _populate_registrations_from_metadata(datasets: dict[str, Dataset]) -> None:
+    from hoa_tools.registration import Inventory, build_transform
+
+    Inventory._clear()  # noqa: SLF001
+    for dataset_name in datasets:
+        dataset = _DATASETS[dataset_name]
+        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,
+                )
+                continue
+            target_dataset = _DATASETS[registration.target_dataset]
+            transform = build_transform(
+                translation=PhysicalCoordinate(
+                    x=registration.translation[0] * target_dataset.data.voxel_size_um,
+                    y=registration.translation[1] * target_dataset.data.voxel_size_um,
+                    z=registration.translation[2] * target_dataset.data.voxel_size_um,
+                ),
+                rotation_deg=registration.rotation,
+                scale=registration.scale
+                * target_dataset.data.voxel_size_um
+                / source_dataset.data.voxel_size_um,
+            )
+            Inventory.add_registration(
+                source_dataset=_DATASETS[registration.source_dataset],
+                target_dataset=_DATASETS[registration.target_dataset],
+                transform=transform,
+            )
+
+
+_META_DIR = Path(__file__).parent / "data" / "metadata" / "metadata"
+try:
+    change_metadata_directory(_META_DIR)
+except FileNotFoundError as e:
+    raise ImportError(
+        "Did not find any dataset metadata files. "
+        "This means there is something wrong with the hoa-tools installation.\n"
+        "Please report this at https://github.com/HumanOrganAtlas/hoa-tools\n"
+        "If you are installing from source, you might need to "
+        "initialise and fetch git submodules. "
+    ) from e

hoa_tools/registration.py

@@ -11,7 +11,7 @@ Transforms are defined using the `SimpleITK` library.
 import numpy as np
 import SimpleITK as sitk
 
-from hoa_tools.dataset import _DATASETS, Dataset
+from hoa_tools.dataset import Dataset
 from hoa_tools.types import PhysicalCoordinate
 
 
@@ -64,6 +64,12 @@ class RegistrationInventory:
             transform.GetInverse()  # type: ignore[no-untyped-call]
         )
 
+    def _clear(self) -> None:
+        """
+        Remove all registrations.
+        """
+        self._registrations = {}
+
 
 def build_transform(
     *, translation: PhysicalCoordinate, rotation_deg: float, scale: float
@@ -83,30 +89,3 @@ def build_transform(
 
 
 Inventory = RegistrationInventory()
-
-
-def _populate_registrations_from_metadata(inventory: RegistrationInventory) -> None:
-    for dataset_name in _DATASETS:
-        dataset = _DATASETS[dataset_name]
-        if (registration := dataset.registration) is not None:
-            source_dataset = _DATASETS[registration.source_dataset]
-            target_dataset = _DATASETS[registration.target_dataset]
-            transform = build_transform(
-                translation=PhysicalCoordinate(
-                    x=registration.translation[0] * target_dataset.data.voxel_size_um,
-                    y=registration.translation[1] * target_dataset.data.voxel_size_um,
-                    z=registration.translation[2] * target_dataset.data.voxel_size_um,
-                ),
-                rotation_deg=registration.rotation,
-                scale=registration.scale
-                * target_dataset.data.voxel_size_um
-                / source_dataset.data.voxel_size_um,
-            )
-            Inventory.add_registration(
-                source_dataset=_DATASETS[registration.source_dataset],
-                target_dataset=_DATASETS[registration.target_dataset],
-                transform=transform,
-            )
-
-
-_populate_registrations_from_metadata(Inventory)

{hoa_tools-1.0.1.dist-info → hoa_tools-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0.1
+Version: 1.0.2
 Summary: Tools for working with the Human Organ Atlas
 Author-email: David Stansby <d.stansby@ucl.ac.uk>
 License: Copyright (c) 2024, David Stansby