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| 1 | +# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- |
| 2 | +# vi: set ft=python sts=4 ts=4 sw=4 et: |
| 3 | +### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## |
| 4 | +# |
| 5 | +# See COPYING file distributed along with the NiBabel package for the |
| 6 | +# copyright and license terms. |
| 7 | +# |
| 8 | +### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## |
| 9 | +""" |
| 10 | +Data structures for the X5 transform format. |
| 11 | +
|
| 12 | +Implements what's drafted in the `BIDS X5 specification draft |
| 13 | +<https://docs.google.com/document/d/1yk5O0QTAOXLdP9iSG3W8ta7IcMFypu2106c3Pnjfi-4/edit>`__. |
| 14 | +
|
| 15 | +""" |
| 16 | + |
| 17 | +from __future__ import annotations |
| 18 | + |
| 19 | +from dataclasses import dataclass |
| 20 | +from pathlib import Path |
| 21 | +from typing import Any, Dict, Optional, Sequence, List |
| 22 | + |
| 23 | +import json |
| 24 | +import h5py |
| 25 | + |
| 26 | +import numpy as np |
| 27 | + |
| 28 | + |
| 29 | +@dataclass |
| 30 | +class X5Domain: |
| 31 | + """Domain information of a transform representing reference/moving spaces.""" |
| 32 | + |
| 33 | + grid: bool |
| 34 | + """Whether sampling locations in the manifold are located regularly.""" |
| 35 | + size: Sequence[int] |
| 36 | + """The number of sampling locations per dimension (or total if not a grid).""" |
| 37 | + mapping: Optional[np.ndarray] |
| 38 | + """A mapping to go from samples (pixel/voxel coordinates, indices) to space coordinates.""" |
| 39 | + coordinates: Optional[str] = None |
| 40 | + """Indexing type of the Mapping field (for example, "cartesian", "spherical" or "index").""" |
| 41 | + |
| 42 | + |
| 43 | +@dataclass |
| 44 | +class X5Transform: |
| 45 | + """Represent one transform entry of an X5 file.""" |
| 46 | + |
| 47 | + type: str |
| 48 | + """A REQUIRED unicode string with possible values: "linear", "nonlinear", "composite".""" |
| 49 | + transform: np.ndarray |
| 50 | + """A REQUIRED array of parameters (e.g., affine matrix, or dense displacements field).""" |
| 51 | + subtype: Optional[str] = None |
| 52 | + """An OPTIONAL extension of type to drive the interpretation of AdditionalParameters.""" |
| 53 | + representation: Optional[str] = None |
| 54 | + """ |
| 55 | + A string specifiying the transform representation or model, REQUIRED only for nonlinear Type. |
| 56 | + """ |
| 57 | + metadata: Optional[Dict[str, Any]] = None |
| 58 | + """An OPTIONAL string (JSON) to embed metadata.""" |
| 59 | + dimension_kinds: Optional[Sequence[str]] = None |
| 60 | + """Identifies what "kind" of information is represented by the samples along each axis.""" |
| 61 | + domain: Optional[X5Domain] = None |
| 62 | + """ |
| 63 | + A dataset specifying the reference manifold for the transform (either |
| 64 | + a regularly gridded 3D space or a surface/sphere). |
| 65 | + REQUIRED for nonlinear Type, RECOMMENDED for linear Type. |
| 66 | + """ |
| 67 | + inverse: Optional[np.ndarray] = None |
| 68 | + """Placeholder to pre-calculated inverses.""" |
| 69 | + jacobian: Optional[np.ndarray] = None |
| 70 | + """ |
| 71 | + A RECOMMENDED data array to keep cached the determinant of Jacobian of the transform |
| 72 | + in case tools have calculated it. |
| 73 | + For parametric models it is generally possible to obtain it analytically, so this dataset |
| 74 | + could not be as useful in that case. |
| 75 | + """ |
| 76 | + # additional_parameters: Optional[np.ndarray] = None |
| 77 | + # AdditionalParameters is empty in the draft spec - ignore for now. |
| 78 | + # Only documentation ATM is for SubType: |
| 79 | + # The SubType setting enables setting the additional parameters on a dataset called |
| 80 | + # "AdditionalParameters" that hangs directly from this transform node. |
| 81 | + array_length: int = 1 |
| 82 | + """Undocumented field in the draft to enable a single transform group for 4D transforms.""" |
| 83 | + |
| 84 | + |
| 85 | +def to_filename(fname: str | Path, x5_list: List[X5Transform]): |
| 86 | + """ |
| 87 | + Write a list of :class:`X5Transform` objects to an X5 HDF5 file. |
| 88 | +
|
| 89 | + Parameters |
| 90 | + ---------- |
| 91 | + fname : :obj:`os.pathlike` |
| 92 | + The file name (preferably with the ".x5" extension) in which transforms will be stored. |
| 93 | + x5_list : :obj:`list` |
| 94 | + The list of transforms to be stored in the output dataset. |
| 95 | +
|
| 96 | + Returns |
| 97 | + ------- |
| 98 | + fname : :obj:`os.pathlike` |
| 99 | + File containing the transform(s). |
| 100 | +
|
| 101 | + """ |
| 102 | + with h5py.File(str(fname), "w") as out_file: |
| 103 | + out_file.attrs["Format"] = "X5" |
| 104 | + out_file.attrs["Version"] = np.uint16(1) |
| 105 | + tg = out_file.create_group("TransformGroup") |
| 106 | + for i, node in enumerate(x5_list): |
| 107 | + g = tg.create_group(str(i)) |
| 108 | + g.attrs["Type"] = node.type |
| 109 | + g.attrs["ArrayLength"] = node.array_length |
| 110 | + if node.subtype is not None: |
| 111 | + g.attrs["SubType"] = node.subtype |
| 112 | + if node.representation is not None: |
| 113 | + g.attrs["Representation"] = node.representation |
| 114 | + if node.metadata is not None: |
| 115 | + g.attrs["Metadata"] = json.dumps(node.metadata) |
| 116 | + g.create_dataset("Transform", data=node.transform) |
| 117 | + g.create_dataset( |
| 118 | + "DimensionKinds", |
| 119 | + data=np.asarray(node.dimension_kinds, dtype="S"), |
| 120 | + ) |
| 121 | + if node.domain is not None: |
| 122 | + dgrp = g.create_group("Domain") |
| 123 | + dgrp.create_dataset("Grid", data=np.uint8(1 if node.domain.grid else 0)) |
| 124 | + dgrp.create_dataset("Size", data=np.asarray(node.domain.size)) |
| 125 | + dgrp.create_dataset("Mapping", data=node.domain.mapping) |
| 126 | + if node.domain.coordinates is not None: |
| 127 | + dgrp.attrs["Coordinates"] = node.domain.coordinates |
| 128 | + |
| 129 | + if node.inverse is not None: |
| 130 | + g.create_dataset("Inverse", data=node.inverse) |
| 131 | + if node.jacobian is not None: |
| 132 | + g.create_dataset("Jacobian", data=node.jacobian) |
| 133 | + # Disabled until we need SubType and AdditionalParameters |
| 134 | + # if node.additional_parameters is not None: |
| 135 | + # g.create_dataset( |
| 136 | + # "AdditionalParameters", data=node.additional_parameters |
| 137 | + # ) |
| 138 | + return fname |
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