brkraw-sordino 0.1.3__py3-none-any.whl

brkraw_sordino/specs/info_spec.yaml

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+__meta__:
+  name: "sordino_info"
+  version: "0.2.0"
+  description: "Scan info spec for SORDINO, based on brkraw scan.yaml plus tuning parameters."
+  category: "info_spec"
+  transforms_source: "./utils.py"
+
+Method:
+  sources:
+    - file: acqp
+      key: ACQ_method
+  transform: strip_jcamp_string
+
+Protocol:
+  sources:
+    - file: acqp
+      key: ACQ_protocol_name
+  transform: strip_jcamp_string
+
+Dim:
+  sources:
+    - file: acqp
+      key: ACQ_dim
+
+DimDesc:
+  sources:
+    - file: acqp
+      key: ACQ_dim_desc
+  transform: convert_to_list
+
+NumEchoes:
+  sources:
+    - file: acqp
+      key: NECHOES
+
+TE (ms):
+  sources:
+    - file: method
+      key: PVM_EchoTime
+    - file: acqp
+      key: ACQ_echo_time
+  transform: convert_to_list
+
+TR (ms):
+  sources:
+    - file: method
+      key: PVM_RepetitionTime
+    - file: method
+      key: RepetitionTime
+    - file: acqp
+      key: ACQ_repetition_time
+  transform: convert_to_list
+
+FlipAngle (degree):
+  sources:
+    - file: acqp
+      key: ACQ_flip_angle
+
+Shape:
+  sources:
+    - file: method
+      key: PVM_Matrix
+  transform: convert_to_list
+
+FOV (mm):
+  sources:
+    - file: method
+      key: PVM_Fov
+  transform: convert_to_list
+
+NumSlicePack:
+  sources:
+    - file: method
+      key: PVM_NSPacks
+
+SliceOrient:
+  sources:
+    - file: method
+      key: PVM_SPackArrSliceOrient
+  transform: convert_to_list
+
+ReadOrient:
+  sources:
+    - file: method
+      key: PVM_SPackArrReadOrient
+  transform: convert_to_list
+
+SliceDistance (mm):
+  sources:
+    - file: method
+      key: PVM_SPackArrSliceDistance
+  transform: convert_to_list
+
+SliceGap (mm):
+  sources:
+    - file: method
+      key: PVM_SPackArrSliceGap
+  transform: convert_to_list
+
+NumAverage:
+  sources:
+    - file: method
+      key: PVM_NAverages
+
+NumRepeat:
+  sources:
+    - file: method
+      key: PVM_NRepetitions
+
+EncNReceivers:
+  sources:
+    - file: method
+      key: PVM_EncNReceivers
+
+NPoints:
+  sources:
+    - file: method
+      key: NPoints
+
+NPro:
+  sources:
+    - file: method
+      key: NPro
+
+EffBandwidth (Hz):
+  sources:
+    - file: method
+      key: PVM_EffSWh
+
+OverSampling:
+  sources:
+    - file: method
+      key: OverSampling
+
+AcqDelayTotal (us):
+  sources:
+    - file: method
+      key: AcqDelayTotal
+
+UnderSampling:
+  sources:
+    - file: method
+      key: ProUnderSampling
+
+SpatialResolution (mm):
+  sources:
+    - file: method
+      key: PVM_SpatResol
+  transform: convert_to_list
+
+HalfAcquisition:
+  sources:
+    - file: method
+      key: HalfAcquisition
+
+UseOrigin:
+  sources:
+    - file: method
+      key: UseOrigin
+
+Reorder:
+  sources:
+    - file: method
+      key: Reorder

brkraw_sordino/specs/metadata_spec.yaml

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+__meta__:
+  name: "sordino_metadata"
+  version: "0.1.0"
+  description: "Draft metadata mapping for ZTE-based fMRI (BEP proposal alignment)."
+  category: "metadata_spec"
+  transforms_source: "./utils.py"
+
+RepetitionTime:
+  sources:
+    - file: method
+      key: PVM_RepetitionTime
+    - file: method
+      key: RepetitionTime
+  transform: ms_to_s
+
+EchoTime:
+  sources:
+    - file: method
+      key: PVM_EchoTime
+  transform: ms_to_s
+
+FlipAngle:
+  sources:
+    - file: acqp
+      key: ACQ_flip_angle
+  transform: first_float
+
+MRAcquisitionType:
+  inputs:
+    value:
+      const: "3D"
+  transform: value_only
+
+Manufacturer:
+  inputs:
+    value:
+      const: "Bruker"
+  transform: value_only
+
+SequenceName:
+  sources:
+    - file: method
+      key: Method
+  transform: strip_bruker_string
+
+ZTETechnique:
+  inputs:
+    method:
+      sources:
+        - file: method
+          key: Method
+        - file: method
+          key: PULPROG
+  transform: infer_zte_technique
+
+ZTETrajectoryType:
+  sources:
+    - file: method
+      key: PVM_TrajType
+    - file: method
+      key: PVM_EncTraj
+    - file: method
+      key: TrajType
+  transform: normalize_trajectory
+
+ZTEReadoutPoints:
+  sources:
+    - file: method
+      key: NPoints
+  transform: first_int
+
+ZTEProjections:
+  sources:
+    - file: method
+      key: NPro
+  transform: first_int
+
+ZTEOverSampling:
+  sources:
+    - file: method
+      key: OverSampling
+  transform: first_float
+
+ZTEEffectiveBandwidth:
+  sources:
+    - file: method
+      key: PVM_EffSWh
+  transform: first_float
+
+ZTEAcqDelayTotal:
+  sources:
+    - file: method
+      key: AcqDelayTotal
+  transform: first_float
+
+ZTEUnderSampling:
+  sources:
+    - file: method
+      key: ProUnderSampling
+  transform: first_float
+
+ZTEReceiverChannels:
+  sources:
+    - file: method
+      key: PVM_EncNReceivers
+  transform: first_int
+
+ReconMatrix:
+  sources:
+    - file: method
+      key: PVM_Matrix
+  transform: to_int_list
+
+FieldOfView:
+  sources:
+    - file: method
+      key: PVM_Fov
+  transform: to_float_list
+
+SpatialResolution:
+  sources:
+    - file: method
+      key: PVM_SpatResol
+  transform: to_float_list
+
+SliceOrientation:
+  sources:
+    - file: method
+      key: PVM_SPackArrSliceOrient
+  transform: convert_to_list
+
+ReadoutOrientation:
+  sources:
+    - file: method
+      key: PVM_SPackArrReadOrient
+  transform: convert_to_list
+
+ConversionSoftware:
+  inputs:
+    value:
+      const: "brkraw-sordino"
+  transform: value_only
+
+ConversionSoftwareVersion:
+  inputs:
+    value:
+      const: "brkraw-sordino"
+  transform: plugin_version
+
+ConversionMethod:
+  inputs:
+    package:
+      const: "brkraw-sordino"
+    name:
+      const: "brkraw-sordino"
+  transform: conversion_method
+
+SourceDataset:
+  inputs:
+    value:
+      const: null
+  transform: source_dataset_env
+
+ScanIdentifier:
+  inputs:
+    scan_id: "$scan_id"
+  transform: scan_id_to_string

brkraw_sordino/specs/prune4recon.yaml

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+__meta__:
+  name: "prune4recon"
+  version: "0.1.0"
+  description: >
+    De-identification pruner spec for Bruker ParaVision datasets that preserves the 
+    FID file for reconstruction purposes. The spec drops the subject file and redacts 
+    potential PII from JCAMP-DX parameters. Supports template variables: 
+    $subject_id, $subject_name, $study_id.
+  category: "pruner_spec"
+
+mode: "keep"
+
+files:
+  - "method"
+  - "acqp"
+  - "reco"
+  - "rawdata.job0"
+  - "visu_pars"
+  - "2dseq"
+
+update_params:
+  acqp:
+    ACQ_operator: ""
+    ACQ_institution: ""
+    ACQ_station: ""
+    ACQ_time: "<00:00:00 01 Jan 2000>"
+    ACQ_abs_time: "0"
+
+  visu_pars:
+    VisuInstitution: ""
+    VisuSubjectId: "$subject_id"
+    VisuSubjectName: "$subject_name"
+    VisuStudyId: "$study_id"
+    VisuStudyDate: "<00:00:00 01 Jan 2000>"
+    VisuStudyUid: "<1.2.3.4.5>"
+    VisuSeriesUid: "<1.2.3.4.5.1>"
+    VisuFrameUid: "<1.2.3.4.5.2>"
+    VisuSystemOrderNumber: "<>"
+    VisuInstitution: "<>"
+
+  reco:
+    RECO_base_image_uid: "<1.2.3.4.5.6>"
+
+add_root: true

brkraw_sordino/specs/recon_spec.yaml

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+__meta__:
+  name: "sordino_recon"
+  version: "0.1.0"
+  description: "Parameter mapping for SORDINO reconstruction."
+  category: "recon_spec"
+  transforms_source: "./utils.py"
+
+SliceOrientation:
+  sources:
+    - file: method
+      key: PVM_SPackArrSliceOrient
+  transform: first
+
+ReadoutOrientation:
+  sources:
+    - file: method
+      key: PVM_SPackArrReadOrient
+  transform: first
+
+GradientOrientation:
+  sources:
+    - file: method
+      key: PVM_SPackArrGradOrient
+  transform: squeeze_ndarray
+
+EncNReceivers:
+  sources:
+    - file: method
+      key: PVM_EncNReceivers
+  transform: first_int
+
+NPoints:
+  sources:
+    - file: method
+      key: NPoints
+  transform: first_int
+
+NPro:
+  sources:
+    - file: method
+      key: NPro
+  transform: first_int
+
+RepetitionTime_ms:
+  sources:
+    - file: method
+      key: RepetitionTime
+    - file: method
+      key: PVM_RepetitionTime
+  transform: first_float
+
+EffBandwidth_Hz:
+  sources:
+    - file: method
+      key: PVM_EffSWh
+  transform: first_float
+
+OverSampling:
+  sources:
+    - file: method
+      key: OverSampling
+  transform: first_float
+
+AcqDelayTotal_us:
+  sources:
+    - file: method
+      key: AcqDelayTotal
+  transform: first_float
+
+NRepetitions:
+  sources:
+    - file: method
+      key: PVM_NRepetitions
+  transform: first_int
+
+Matrix:
+  sources:
+    - file: method
+      key: PVM_Matrix
+
+UnderSampling:
+  sources:
+    - file: method
+      key: ProUnderSampling
+  transform: first_float
+
+HalfAcquisition:
+  sources:
+    - file: method
+      key: HalfAcquisition
+  transform: to_bool
+
+UseOrigin:
+  sources:
+    - file: method
+      key: UseOrigin
+  transform: to_bool
+
+Reorder:
+  sources:
+    - file: method
+      key: Reorder
+  transform: to_bool

brkraw_sordino/specs/utils.py

@@ -0,0 +1,212 @@
+"""Transform helpers for brkraw-sordino metadata and info mapping."""
+
+from __future__ import annotations
+
+import os
+import re
+import numpy as np
+from typing import Any, Optional, cast
+from importlib import metadata
+
+
+def squeeze_ndarray(value: np.ndarray) -> np.ndarray:
+    return value.squeeze()
+
+
+def strip_bruker_string(value: Any) -> Any:
+    if value is None:
+        return None
+    text = str(value).strip()
+    if text.startswith("<") and text.endswith(">"):
+        text = text[1:-1]
+    return text.strip()
+
+
+def strip_jcamp_string(value: Optional[str]) -> str:
+    if value is None:
+        return "Unknown"
+    text = str(value).strip()
+    if text.startswith("<") and text.endswith(">"):
+        text = text[1:-1]
+    text = re.sub(r"\^+", " ", text)
+    return " ".join(text.split())
+
+
+def ensure_list(value: Any) -> Optional[list]:
+    if value is None:
+        return None
+    if isinstance(value, (list, tuple)):
+        return list(value)
+    return [value]
+
+
+def convert_to_list(value: Any):
+    if value is None:
+        return []
+    if hasattr(value, "tolist"):
+        return cast(Any, value).tolist()
+    if isinstance(value, (list, tuple)):
+        return list(value)
+    return [value]
+
+
+def first(value: Any) -> Any:
+    if value is None:
+        return None
+    if isinstance(value, (list, tuple)) and value:
+        return value[0]
+    try:
+        import numpy as np
+        if isinstance(value, np.ndarray) and value.size:
+            return value.flat[0]
+    except Exception:
+        pass
+    return value
+
+
+def first_float(value: Any) -> Optional[float]:
+    val = first(value)
+    if val is None:
+        return None
+    try:
+        return float(val)
+    except Exception:
+        return None
+
+
+def first_int(value: Any) -> Optional[int]:
+    val = first(value)
+    if val is None:
+        return None
+    try:
+        return int(val)
+    except Exception:
+        return None
+
+
+def to_float_list(value: Any) -> Optional[list]:
+    values = ensure_list(value)
+    if values is None:
+        return None
+    out = []
+    for item in values:
+        try:
+            out.append(float(item))
+        except Exception:
+            return None
+    return out
+
+
+def to_int_list(value: Any) -> Optional[list]:
+    values = ensure_list(value)
+    if values is None:
+        return None
+    out = []
+    for item in values:
+        try:
+            out.append(int(item))
+        except Exception:
+            return None
+    return out
+
+
+def to_bool(value: Any) -> bool:
+    if isinstance(value, str):
+        return value.strip().lower() in {"yes", "true", "1", "on"}
+    return bool(value)
+
+
+def ms_to_s(value: Any) -> Optional[float]:
+    val = first_float(value)
+    if val is None:
+        return None
+    return val * 1e-3
+
+
+def dwell_time_seconds(*, sw_hz: Any = None, dwell_us: Any = None) -> Optional[float]:
+    sw = first_float(sw_hz)
+    if sw:
+        return 1.0 / sw
+    dwell = first_float(dwell_us)
+    if dwell is None:
+        return None
+    return float(dwell) * 1e-6 * 2.0
+
+
+def lower_string(value: Any) -> Optional[str]:
+    if value is None:
+        return None
+    return str(value).strip().lower()
+
+
+def _normalize_text(value: Any) -> Optional[str]:
+    if value is None:
+        return None
+    text = str(value).strip()
+    return " ".join(text.split()) if text else None
+
+
+def infer_zte_technique(*, method: Any = None, sequence: Any = None) -> Optional[str]:
+    text = _normalize_text(method) or _normalize_text(sequence)
+    if not text:
+        return None
+    lowered = text.lower()
+    if "sordino" in lowered:
+        return "SORDINO"
+    if "swift" in lowered:
+        return "MB-SWIFT"
+    if "zte" in lowered:
+        return "ZTE"
+    return None
+
+
+def normalize_trajectory(value: Any) -> Optional[str]:
+    text = _normalize_text(value)
+    if not text:
+        return None
+    lowered = text.lower()
+    mapping = {
+        "radial": "radial",
+        "spiral": "spiral",
+        "cartesian": "cartesian",
+        "cart": "cartesian",
+        "cones": "cones",
+        "rosette": "rosette",
+    }
+    for key, target in mapping.items():
+        if key in lowered:
+            return target
+    return lowered
+
+
+def value_only(*, value: Any) -> Any:
+    return value
+
+
+def plugin_version(*, value: Any) -> str:
+    pkg = str(value or "brkraw-sordino")
+    try:
+        return metadata.version(pkg)
+    except Exception:
+        return "unknown"
+
+
+def conversion_method(*, package: Any = None, name: Any = None) -> str:
+    pkg = str(package or name or "brkraw-sordino")
+    base = str(name or pkg)
+    try:
+        version = metadata.version(pkg)
+    except Exception:
+        version = None
+    return f"{base} v{version}" if version else base
+
+
+def source_dataset_env(*, value: Any) -> Optional[str]:
+    _ = value
+    return os.environ.get("BRKRAW_SOURCE_DATASET")
+
+
+def scan_id_to_string(*, scan_id: Any) -> Optional[str]:
+    if scan_id is None:
+        return None
+    return str(scan_id)