diff --git a/brukerapi/__init__.py b/brukerapi/__init__.py index f286645..fde5579 100644 --- a/brukerapi/__init__.py +++ b/brukerapi/__init__.py @@ -1 +1 @@ -__all__ = ["dataset","exceptions","filters","folders", "jcampdx","schemes","utils"] \ No newline at end of file +__all__ = ["dataset", "exceptions", "folders", "jcampdx", "utils"] diff --git a/brukerapi/cli.py b/brukerapi/cli.py index 7677968..eaf6a4b 100644 --- a/brukerapi/cli.py +++ b/brukerapi/cli.py @@ -129,12 +129,12 @@ def report(args): if input.is_dir(): # folder in-place if output is None: - Folder(input).report(format_=args.format, props=args.props, verbose=args.verbose) + Folder(str(input)).report(format_=args.format, props=args.props, verbose=args.verbose) else: # folder to folder -- an output folder that does not exist yet is # created rather than silently matching no branch and exiting 0 output.mkdir(parents=True, exist_ok=True) - Folder(input).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose) + Folder(str(input)).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose) # dataset in-place elif output is None: Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose, format_=args.format) diff --git a/brukerapi/folders.py b/brukerapi/folders.py index f12562a..2b2dc14 100644 --- a/brukerapi/folders.py +++ b/brukerapi/folders.py @@ -29,8 +29,8 @@ class Folder: def __init__( self, - path: str, - parent: "Folder" = None, + path: str | Path, + parent: "Folder | None" = None, recursive: bool | None = None, # noqa: FBT001 dataset_index: list | None = None, dataset_state: dict | None = None, @@ -147,8 +147,9 @@ def query(self, query): self.clean(node=self) - def query_pass(self, query: str, node: "Folder" = None): - children_out = [] + def query_pass(self, query: str, node: "Folder | None" = None): + node = self if node is None else node + children_out: list[Folder | Dataset | JCAMPDX] = [] for child in node.children: if isinstance(child, Folder): children_out.append(self.query_pass(query, node=child)) @@ -164,7 +165,7 @@ def query_pass(self, query: str, node: "Folder" = None): node.children = children_out return node - def clean(self, node: "Folder" = None) -> "Folder": + def clean(self, node: "Folder | None" = None) -> "Folder": """Remove empty folders from the tree :param node: @@ -208,9 +209,9 @@ def get_study_list(self) -> list: """List of :obj:`.Study` instances contained in folder and its sub-folders""" return TypeFilter(Study).list(self) - def make_tree(self, *, recursive: bool = True) -> list: + def make_tree(self, *, recursive: bool = True) -> list["Folder | Dataset | JCAMPDX"]: """Build a folder tree with optimized traversal.""" - children = [] + children: list[Folder | Dataset | JCAMPDX] = [] entries = list(self.path.iterdir()) for path in entries: @@ -334,8 +335,8 @@ class Study(Folder): def __init__( self, - path: str, - parent: "Folder" = None, + path: str | Path, + parent: "Folder | None" = None, recursive: bool | None = None, # noqa: FBT001 dataset_index: list | None = None, dataset_state: dict | None = None, @@ -415,8 +416,8 @@ class Experiment(Folder): def __init__( self, - path: str, - parent: "Folder" = None, + path: str | Path, + parent: "Folder | None" = None, recursive: bool | None = None, # noqa: FBT001 dataset_index: list | None = None, dataset_state: dict | None = None, @@ -463,7 +464,14 @@ def _get_proc(self, proc_id): class Processing(Folder): - def __init__(self, path, parent=None, recursive=None, dataset_index=None, dataset_state: dict | None = None): + def __init__( + self, + path: str | Path, + parent: "Folder | None" = None, + recursive: bool | None = None, # noqa: FBT001 + dataset_index: list | None = None, + dataset_state: dict | None = None, + ): """The constructor for Processing class. :param path: path to a folder diff --git a/brukerapi/mergers.py b/brukerapi/mergers.py index 297dda9..4ff04dd 100644 --- a/brukerapi/mergers.py +++ b/brukerapi/mergers.py @@ -47,8 +47,8 @@ def _merge_data(cls, dataset, fg_abs_index): :param fg_abs_index: index of dimension of the data array to be merged :return: """ - slc_re = [slice(None, None, None) for _ in range(dataset.data.ndim)] - slc_im = [slice(None, None, None) for _ in range(dataset.data.ndim)] + slc_re: list[slice | int] = [slice(None, None, None) for _ in range(dataset.data.ndim)] + slc_im: list[slice | int] = [slice(None, None, None) for _ in range(dataset.data.ndim)] slc_re[fg_abs_index] = 0 slc_im[fg_abs_index] = 1 diff --git a/brukerapi/utils.py b/brukerapi/utils.py index 4070529..c4a660c 100644 --- a/brukerapi/utils.py +++ b/brukerapi/utils.py @@ -59,6 +59,8 @@ def simple_measurement(dataset): axes = (0, 1) elif dataset.encoded_dim == 3: axes = (0, 1, 2) + else: + raise ValueError("Simple measurement supports one to three encoded dimensions") return np.fft.fftshift(np.fft.fft2(dataset.data, axes=axes), axes=axes) @@ -74,6 +76,8 @@ def simple_reconstruction(dataset, **kwargs): axes = (0, 1) elif dataset.encoded_dim == 3: axes = (0, 1, 2) + else: + raise ValueError("Simple reconstruction supports one to three encoded dimensions") data = np.fft.fftshift(np.fft.ifft2(dataset.data, axes=axes), axes=axes) diff --git a/docs/source/compatibility.rst b/docs/source/compatibility.rst index 3dd1ce9..f3b1f04 100644 --- a/docs/source/compatibility.rst +++ b/docs/source/compatibility.rst @@ -45,13 +45,22 @@ Data contract and limitations * FID data is returned as ordered raw k-space. ``AQ_mod=qf`` remains real; quadrature modes are assembled as complex data. -* RARE/EPI phase-line ordering and EPI odd-line mirroring are applied. - Ramp-sampling regridding and ``RECO_qopts`` corrections are not full - reconstruction steps and remain the caller's responsibility. +* RARE/EPI phase-line ordering and EPI odd-line mirroring are applied. The + reader uses ``ACQ_scan_size`` and the selected reconstruction's + ``RECO_inp_order`` when available; pulse-program scheme inference is the + fallback for a FID without a reconstruction. The default reconstruction is + the conventional first one, and ``reco_path=`` selects a different ``reco`` + file. A disagreement between explicit metadata and the fallback inference + emits ``RuntimeWarning``. Ramp-sampling regridding and ``RECO_qopts`` + corrections are not full reconstruction steps and remain the caller's + responsibility. * Rawdata jobs are returned as complex ordered samples in their stored job layout through ``data``. Prefer ``raw`` for the normalized ``(sample, shot, receiver)`` acquisition stream and ``kspace`` for validated - Cartesian PV360 layout conversion. + Cartesian PV360 layout conversion. ``STORE_discard`` jobs are omitted from + folder discovery because no binary exists. When both records are present, + ``ACQ_ScanPipeJobSettings.nStoredScans`` determines the stored shape and is + checked against ``ACQ_jobs``; the per-job receiver selection is also read. * 2dseq values are scaled as ``stored * slope + offset``. Visu slopes/offsets take precedence, with RECO values as fallback. * PV7/PV360 2dseq geometry uses the version-independent Visu geometry fields. @@ -86,4 +95,7 @@ Data contract and limitations ``UnsupportedDatasetType`` rather than returning an identity matrix. A dataset with several slice packages cannot be described by one affine; it warns, and ``affine_of_package(i)`` or ``slice_packages`` gives the - per-package transform. + per-package transform. If optional slice-package metadata is absent (notably + in PV5.1), contiguous frames with a common orientation are treated as one + package. Consequently two adjacent inferred packages with the same + orientation cannot be distinguished. diff --git a/docs/source/tutorials/how-to-2dseq.rst b/docs/source/tutorials/how-to-2dseq.rst index d035eba..cb0d85a 100644 --- a/docs/source/tutorials/how-to-2dseq.rst +++ b/docs/source/tutorials/how-to-2dseq.rst @@ -63,6 +63,12 @@ in-memory datasets, including their own geometry, with: for package in dataset.slice_packages: print(package.data.shape, package.affine, package.resolution) +This also works for older PV5.1 datasets that do not have the optional +``VisuCoreSlicePacks*`` parameters. In that case packages are inferred from +contiguous frames with the same orientation. This inference cannot distinguish +two immediately adjacent packages that share an orientation; PV6 and later +datasets use the explicit package descriptors when available. + Use memory-mapped random access when only a sub-array is needed: .. code-block:: python diff --git a/docs/source/tutorials/how-to-fid.rst b/docs/source/tutorials/how-to-fid.rst index 1b6f6ba..5d62735 100644 --- a/docs/source/tutorials/how-to-fid.rst +++ b/docs/source/tutorials/how-to-fid.rst @@ -33,6 +33,24 @@ Use the explicit views in new code: ``dataset.raw`` is the decoded acquisition stream with axes ``(sample, shot, receiver)``; ``dataset.kspace`` is the same ordered k-space exposed through ``data`` for compatibility. +When an experiment has a reconstruction, its ``reco`` declaration is used to +determine EPI continuous-train handling and odd-line reversal +(``RECO_inp_order=REV_ALT_ROWS``). The conventional first reconstruction is +used by default. Select another reconstruction explicitly when its input-order +metadata is the one that corresponds to the data being read: + +.. code-block:: python + + dataset = Dataset( + 'path/to/fid', + reco_path='path/to/pdata/2/reco', + ) + +For a FID without a reconstruction, the reader falls back to the acquisition +declaration and, where necessary, the pulse-program scheme inference. A +``RuntimeWarning`` is emitted if the selected ``reco`` and scheme inference +disagree; the declared reconstruction value is used. + For custom pulse-program names the scheme is inferred from acquisition metadata. An explicit override is available when inference is ambiguous: diff --git a/docs/source/tutorials/how-to-rawdata.rst b/docs/source/tutorials/how-to-rawdata.rst index eb47a1c..26db5f1 100644 --- a/docs/source/tutorials/how-to-rawdata.rst +++ b/docs/source/tutorials/how-to-rawdata.rst @@ -31,3 +31,18 @@ metadata-reordered array. BART consumers can request its 16-axis layout: decoded job layout. It emits ``FutureWarning`` because that layout differs from FID ``data``. Prefer ``raw`` or ``kspace`` in new applications. EPI and non-Cartesian jobs are not reconstructed by ``kspace``. + +Job discovery honours ``ACQ_ScanPipeJobSettings``. Jobs marked +``STORE_discard`` are deliberately omitted because ParaVision does not write a +corresponding ``rawdata.jobN`` file. For a present job, the reader sizes its +data from the settings record's ``nStoredScans`` and exposes the relevant +per-job metadata: + +.. code-block:: python + + settings = rawdata.rawdata_job_settings + scans = rawdata.rawdata_stored_scans + receivers = rawdata.rawdata_channels + +If the settings and ``ACQ_jobs`` records disagree about the stored scan count, +the settings value is used and a ``RuntimeWarning`` identifies the mismatch. diff --git a/poetry.lock b/poetry.lock index 92d4129..e782f38 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,169 @@ # This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. +[[package]] +name = "anyio" +version = "4.14.2" +description = "High-level concurrency and networking framework on top of asyncio or Trio" +optional = true +python-versions = ">=3.10" +groups = ["main"] +markers = "extra == \"dev\"" +files = [ + {file = "anyio-4.14.2-py3-none-any.whl", hash = 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