brkraw 0.3.11__py3-none-any.whl → 0.5.0__py3-none-any.whl

brkraw/schema/meta.yaml

@@ -0,0 +1,57 @@
+---
+$schema: "https://json-schema.org/draft/2020-12/schema"
+title: "BrkRaw Spec Metadata"
+type: object
+additionalProperties: false
+required:
+  - name
+  - version
+  - description
+  - category
+properties:
+  name:
+    type: string
+    pattern: "^[a-z][a-z0-9]*(?:_[a-z0-9]+){0,3}$"
+    description: "Python-friendly identifier (max 4 tokens)."
+  version:
+    type: string
+    minLength: 1
+  description:
+    type: string
+    minLength: 1
+  category:
+    type: string
+    minLength: 1
+  authors:
+    type: array
+    items:
+      $ref: "#/$defs/person"
+    minItems: 1
+  developers:
+    type: array
+    items:
+      $ref: "#/$defs/person"
+    minItems: 1
+  doi:
+    type: string
+  citation:
+    type: string
+$defs:
+  person:
+    type: object
+    additionalProperties: false
+    required:
+      - name
+    properties:
+      name:
+        type: string
+        minLength: 1
+      email:
+        type: string
+        minLength: 1
+      affiliations:
+        type: array
+        items:
+          type: string
+          minLength: 1
+        minItems: 1

brkraw/schema/niftiheader.yaml

@@ -0,0 +1,95 @@
+---
+$schema: "https://json-schema.org/draft/2020-12/schema"
+title: "BrkRaw NIfTI Header Overrides"
+type: object
+additionalProperties: false
+properties:
+  flip_x:
+    type: boolean
+  slice_code:
+    type: integer
+  slope_inter:
+    type: array
+    items:
+      type: number
+    minItems: 2
+    maxItems: 2
+  time_step:
+    type:
+      - number
+      - "null"
+  slice_duration:
+    type:
+      - number
+      - "null"
+  xyzt_unit:
+    type: array
+    items:
+      - $ref: "#/$defs/xyz_unit"
+      - $ref: "#/$defs/t_unit"
+    minItems: 2
+    maxItems: 2
+  qform:
+    $ref: "#/$defs/matrix4x4"
+  sform:
+    $ref: "#/$defs/matrix4x4"
+  qform_code:
+    type: integer
+  sform_code:
+    type: integer
+  dim_info:
+    type: array
+    items:
+      type:
+        - integer
+        - "null"
+    minItems: 3
+    maxItems: 3
+  slice_start:
+    type: integer
+  slice_end:
+    type: integer
+  intent_code:
+    type: integer
+  intent_name:
+    type: string
+  descrip:
+    type: string
+  aux_file:
+    type: string
+  cal_min:
+    type: number
+  cal_max:
+    type: number
+  pixdim:
+    type: array
+    items:
+      type: number
+    minItems: 1
+$defs:
+  xyz_unit:
+    type: string
+    enum:
+      - unknown
+      - meter
+      - mm
+      - micron
+  t_unit:
+    type: string
+    enum:
+      - sec
+      - msec
+      - usec
+      - hz
+      - ppm
+      - rads
+  matrix4x4:
+    type: array
+    minItems: 4
+    maxItems: 4
+    items:
+      type: array
+      minItems: 4
+      maxItems: 4
+      items:
+        type: number

brkraw/schema/pruner.yaml

@@ -0,0 +1,55 @@
+---
+$schema: "https://json-schema.org/draft/2020-12/schema"
+title: "BrkRaw Pruner Spec"
+type: object
+additionalProperties: false
+properties:
+  __meta__:
+    type: object
+    additionalProperties: true
+  files:
+    type: array
+    minItems: 1
+    items:
+      type:
+        - string
+        - number
+  mode:
+    type: string
+    enum: ["keep", "drop"]
+  update_params:
+    type: object
+    additionalProperties:
+      type: object
+      additionalProperties:
+        type:
+          - string
+          - number
+          - boolean
+          - "null"
+  dirs:
+    type: array
+    items:
+      type: object
+      additionalProperties: false
+      required: ["level", "dirs"]
+      properties:
+        level:
+          type: integer
+          minimum: 1
+        dirs:
+          type: array
+          minItems: 1
+          items:
+            type:
+              - string
+              - number
+  add_root:
+    type: boolean
+  root_name:
+    type: string
+  strip_jcamp_comments:
+    type: boolean
+required:
+  - __meta__
+  - files

brkraw/schema/remapper.yaml

@@ -0,0 +1,128 @@
+$schema: "https://json-schema.org/draft/2020-12/schema"
+title: "BrkRaw Parameter Mapping Spec"
+description: "Map Bruker parameter files into a structured output dict."
+type: object
+properties:
+  __meta__:
+    type: object
+    additionalProperties: true
+    properties:
+      transforms_source:
+        anyOf:
+          - type: string
+          - type: array
+            items:
+              type: string
+      include:
+        anyOf:
+          - type: string
+          - type: array
+            items:
+              type: string
+      include_mode:
+        type: string
+        enum:
+          - override
+          - strict
+required:
+  - __meta__
+additionalProperties:
+  $ref: "#/$defs/Rule"
+
+$defs:
+  Rule:
+    type: object
+    properties:
+      sources:
+        type: array
+        items: { $ref: "#/$defs/SourceItem" }
+        description: "Ordered list of sources to resolve a single output value."
+      inputs:
+        type: object
+        additionalProperties: { $ref: "#/$defs/Input" }
+        description: "Named inputs that are passed to a transform or returned as-is."
+      const: {}
+      ref:
+        type: string
+        description: "Dot path to a previously resolved output value."
+      transform:
+        anyOf:
+          - type: string
+          - type: array
+            items: { type: string }
+        description: "Transform name(s) to apply. Arrays execute in order."
+      default: {}
+    additionalProperties: false
+    oneOf:
+      - required: ["sources"]
+      - required: ["inputs"]
+      - required: ["const"]
+      - required: ["ref"]
+
+  Source:
+    type: object
+    properties:
+      file:
+        type: string
+        enum: ["method", "acqp", "visu_pars", "reco", "subject"]
+        description: "Parameter file namespace."
+      key:
+        type: string
+        description: "Key name in the parameter file."
+      reco_id:
+        type: integer
+        minimum: 1
+        description: "Reco id used when file targets reco-specific data."
+    required: ["file", "key"]
+    additionalProperties: false
+  SourceItem:
+    anyOf:
+      - $ref: "#/$defs/Source"
+      - $ref: "#/$defs/InlineInputs"
+
+  InlineInputs:
+    type: object
+    properties:
+      inputs:
+        type: object
+        additionalProperties: { $ref: "#/$defs/Input" }
+        description: "Named inputs that are passed to a transform or returned as-is."
+      transform:
+        anyOf:
+          - type: string
+          - type: array
+            items: { type: string }
+        description: "Transform name(s) to apply. Arrays execute in order."
+    additionalProperties: false
+    required: ["inputs"]
+
+  Input:
+    anyOf:
+      - type: string
+        pattern: "^\\$[A-Za-z_][A-Za-z0-9_]*$"
+        description: "Context variable reference (e.g., $scan_id)."
+      - type: object
+        properties:
+          sources:
+            type: array
+            items: { $ref: "#/$defs/Source" }
+            description: "Ordered list of sources to resolve an input value."
+          const: {}
+          ref:
+            type: string
+            description: "Dot path to a previously resolved output value."
+          transform:
+            anyOf:
+              - type: string
+              - type: array
+                items: { type: string }
+            description: "Transform name(s) to apply. Arrays execute in order."
+          default: {}
+          required:
+            type: boolean
+            description: "If true, missing input raises instead of returning None."
+        additionalProperties: false
+        oneOf:
+          - required: ["sources"]
+          - required: ["const"]
+          - required: ["ref"]

brkraw/schema/rules.yaml

@@ -0,0 +1,154 @@
+---
+$schema: "https://json-schema.org/draft/2020-12/schema"
+title: "BrkRaw Rules"
+type: object
+properties:
+  info_spec:
+    $ref: "#/$defs/rule_list"
+  metadata_spec:
+    $ref: "#/$defs/rule_list"
+  converter_hook:
+    $ref: "#/$defs/rule_list"
+additionalProperties: false
+$defs:
+  rule_list:
+    type: array
+    items:
+      $ref: "#/$defs/rule"
+  rule:
+    type: object
+    properties:
+      name:
+        type: string
+        minLength: 1
+      description:
+        type: string
+      version:
+        type: string
+      when:
+        $ref: "#/$defs/when"
+      if:
+        $ref: "#/$defs/expr"
+      use:
+        type: string
+        minLength: 1
+    required:
+      - name
+      - use
+    additionalProperties: false
+  when:
+    type: object
+    minProperties: 1
+    additionalProperties:
+      $ref: "#/$defs/when_binding"
+  when_binding:
+    type: object
+    properties:
+      sources:
+        type: array
+        items:
+          $ref: "#/$defs/source"
+        minItems: 1
+      transform:
+        type: string
+    required:
+      - sources
+    additionalProperties: false
+  source:
+    type: object
+    properties:
+      file:
+        type: string
+        enum:
+          - method
+          - acqp
+          - visu_pars
+          - reco
+          - subject
+      key:
+        type: string
+        minLength: 1
+      reco_id:
+        type: integer
+        minimum: 1
+    required:
+      - file
+      - key
+    additionalProperties: false
+  expr:
+    oneOf:
+      - $ref: "#/$defs/expr_any"
+      - $ref: "#/$defs/expr_all"
+      - $ref: "#/$defs/expr_not"
+      - $ref: "#/$defs/expr_op"
+  expr_any:
+    type: object
+    properties:
+      any:
+        type: array
+        items:
+          $ref: "#/$defs/expr"
+        minItems: 1
+    required:
+      - any
+    additionalProperties: false
+  expr_all:
+    type: object
+    properties:
+      all:
+        type: array
+        items:
+          $ref: "#/$defs/expr"
+        minItems: 1
+    required:
+      - all
+    additionalProperties: false
+  expr_not:
+    type: object
+    properties:
+      not:
+        $ref: "#/$defs/expr"
+    required:
+      - not
+    additionalProperties: false
+  expr_op:
+    type: object
+    minProperties: 1
+    maxProperties: 1
+    properties:
+      eq:
+        $ref: "#/$defs/binop"
+      ne:
+        $ref: "#/$defs/binop"
+      in:
+        $ref: "#/$defs/inop"
+      regex:
+        $ref: "#/$defs/binop"
+      startswith:
+        $ref: "#/$defs/binop"
+      contains:
+        $ref: "#/$defs/binop"
+      always:
+        type: boolean
+      gt:
+        $ref: "#/$defs/binop"
+      ge:
+        $ref: "#/$defs/binop"
+      lt:
+        $ref: "#/$defs/binop"
+      le:
+        $ref: "#/$defs/binop"
+    additionalProperties: false
+  binop:
+    type: array
+    items: {}
+    minItems: 2
+    maxItems: 2
+  inop:
+    type: array
+    prefixItems:
+      - {}
+      - type: array
+    items: false
+    minItems: 2
+    maxItems: 2

brkraw/specs/__init__.py

@@ -0,0 +1,10 @@
+from __future__ import annotations
+
+from . import hook, pruner, remapper, rules
+
+__all__ = [
+    "hook",
+    "pruner",
+    "remapper",
+    "rules",
+]

brkraw/specs/hook/__init__.py

@@ -0,0 +1,12 @@
+from __future__ import annotations
+
+from .logic import DEFAULT_GROUP, resolve_hook
+from .validator import validate_hook, CONVERTER_KEYS
+
+__all__ = [
+    "CONVERTER_KEYS",
+    "DEFAULT_GROUP",
+    "resolve_hook",
+    "validate_hook",
+]
+

brkraw/specs/hook/logic.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from collections.abc import Mapping
+from typing import Any, Callable, Dict, Union
+
+from ...core.entrypoints import list_entry_points
+from .validator import validate_hook
+
+DEFAULT_GROUP = "brkraw.converter_hook"
+
+
+def resolve_hook(
+    hook: Union[Mapping[str, Callable[..., Any]], str],
+    *,
+    group: str = DEFAULT_GROUP,
+) -> Dict[str, Callable[..., Any]]:
+    if isinstance(hook, str):
+        matches = list_entry_points(group, hook)
+        if not matches:
+            raise LookupError(
+                f"Converter hook not found: {hook!r} (group={group!r})"
+            )
+        entry = matches[0].load()
+        validate_hook(entry)
+        return dict(entry)
+    validate_hook(hook)
+    return dict(hook)
+
+
+__all__ = ["DEFAULT_GROUP", "resolve_hook"]
+

brkraw/specs/hook/validator.py

@@ -0,0 +1,22 @@
+from __future__ import annotations
+
+from collections.abc import Mapping
+from typing import Any, List
+
+CONVERTER_KEYS = {"get_dataobj", "get_affine", "convert"}
+
+
+def validate_hook(hook: Any, *, raise_on_error: bool = True) -> List[str]:
+    errors: List[str] = []
+    if not isinstance(hook, Mapping):
+        errors.append("converter_hook: must be a mapping.")
+    else:
+        for key, value in hook.items():
+            if key not in CONVERTER_KEYS:
+                errors.append(f"converter_hook: invalid key {key!r}.")
+            if not callable(value):
+                errors.append(f"converter_hook[{key!r}]: must be callable.")
+    if errors and raise_on_error:
+        raise ValueError("Invalid converter hook:\n" + "\n".join(errors))
+    return errors
+

brkraw/specs/meta/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .validator import validate_meta
+
+__all__ = ["validate_meta"]