brkraw 0.5.0rc1__py3-none-any.whl → 0.5.1__py3-none-any.whl

brkraw/specs/remapper/logic.py

@@ -503,9 +503,15 @@ def map_parameters(
                     val = _apply_inputs_transform(inputs, transforms, rule["transform"])
                 else:
                     val = inputs
-            else:
+            elif "sources" in rule:
                 raw = _resolve_value(source, rule.get("sources", []), transforms, result, ids)
                 val = _apply_transform_chain(raw, transforms, rule.get("transform"))
+            elif "const" in rule:
+                val = _apply_transform_chain(rule.get("const"), transforms, rule.get("transform"))
+            elif "ref" in rule:
+                val = _apply_transform_chain(_get_nested(result, rule["ref"]), transforms, rule.get("transform"))
+            else:
+                val = _apply_transform_chain(rule.get("default"), transforms, rule.get("transform"))
 
             if "." in out_key:
                 _set_nested(result, out_key, val)
@@ -670,34 +676,95 @@ def _apply_map_rules(
 
 def _normalize_map_rules(raw_rule: Any) -> List[Dict[str, Any]]:
     if isinstance(raw_rule, list):
-        return [dict(rule) for rule in raw_rule if isinstance(rule, Mapping)]
+        rules = [dict(rule) for rule in raw_rule if isinstance(rule, Mapping)]
+        return _expand_case_rules(rules)
     if isinstance(raw_rule, Mapping):
-        return [dict(raw_rule)]
+        return _expand_case_rules([dict(raw_rule)])
     raise ValueError("Map rule must be a mapping or list of mappings.")
 
 
 def _is_selector_rule(raw_rule: Any) -> bool:
-    if isinstance(raw_rule, Mapping):
-        return bool(raw_rule.get("selector"))
-    if isinstance(raw_rule, list):
-        return any(isinstance(rule, Mapping) and rule.get("selector") for rule in raw_rule)
-    return False
+    return any(rule.get("selector") for rule in _iter_rule_objects(raw_rule))
 
 
 def _rule_targets(raw_rule: Any) -> Set[str]:
     targets: Set[str] = set()
-    if isinstance(raw_rule, Mapping):
-        value = raw_rule.get("target")
+    for rule in _iter_rule_objects(raw_rule):
+        value = rule.get("target")
         if isinstance(value, str):
             targets.add(value)
+    return targets
+
+
+def _iter_rule_objects(raw_rule: Any) -> Iterable[Mapping[str, Any]]:
+    if isinstance(raw_rule, Mapping):
+        yield raw_rule
+        cases = raw_rule.get("cases")
+        if isinstance(cases, list):
+            for case in cases:
+                yield from _iter_rule_objects(case)
     elif isinstance(raw_rule, list):
         for rule in raw_rule:
-            if not isinstance(rule, Mapping):
-                continue
-            value = rule.get("target")
-            if isinstance(value, str):
-                targets.add(value)
-    return targets
+            yield from _iter_rule_objects(rule)
+
+
+def _expand_case_rules(rules: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    expanded: List[Dict[str, Any]] = []
+    for rule in rules:
+        expanded.extend(_expand_rule_cases(rule))
+    return expanded
+
+
+def _expand_rule_cases(rule: Dict[str, Any]) -> List[Dict[str, Any]]:
+    cases = rule.get("cases")
+    if not isinstance(cases, list):
+        return [dict(rule)]
+    parent = dict(rule)
+    parent.pop("cases", None)
+    expanded: List[Dict[str, Any]] = []
+    for case in cases:
+        if not isinstance(case, Mapping):
+            continue
+        merged = _merge_case_rule(parent, case)
+        if "cases" in merged:
+            expanded.extend(_expand_rule_cases(merged))
+        else:
+            expanded.append(merged)
+    if _rule_has_value(parent):
+        expanded.append(parent)
+    return expanded
+
+
+def _merge_case_rule(parent: Mapping[str, Any], case: Mapping[str, Any]) -> Dict[str, Any]:
+    merged = dict(parent)
+    parent_when = parent.get("when")
+    case_when = case.get("when")
+    if isinstance(parent_when, Mapping) and isinstance(case_when, Mapping):
+        merged["when"] = {**parent_when, **case_when}
+    elif case_when is not None:
+        merged["when"] = case_when
+    elif parent_when is not None:
+        merged["when"] = parent_when
+    for key, value in case.items():
+        if key == "when":
+            continue
+        merged[key] = value
+    return merged
+
+
+def _rule_has_value(rule: Mapping[str, Any]) -> bool:
+    if "value" in rule:
+        return True
+    if "values" in rule:
+        return isinstance(rule.get("values"), Mapping)
+    if "default" in rule and "when" not in rule:
+        return True
+    rule_type = rule.get("type")
+    if rule_type == "const":
+        return "value" in rule
+    if rule_type == "mapping":
+        return isinstance(rule.get("values"), Mapping)
+    return False
 
 
 def _rule_applies_to_target(raw_rule: Any, target: Optional[str]) -> bool:

brkraw/specs/remapper/validator.py

@@ -14,7 +14,7 @@ import yaml
 from ..meta import validate_meta
 
 _ALLOWED_FILES = {"method", "acqp", "visu_pars", "reco", "subject"}
-_RULE_KEYS = {"sources", "inputs", "transform", "default"}
+_RULE_KEYS = {"sources", "inputs", "const", "ref", "transform", "default"}
 _INPUT_KEYS = {"sources", "const", "ref", "transform", "default", "required"}
 _INLINE_SOURCE_KEYS = {"inputs", "transform"}
 _META_KEY = "__meta__"
@@ -154,12 +154,14 @@ def _validate_spec_minimal(spec: Any) -> List[str]:
         extra = set(rule.keys()) - _RULE_KEYS
         if extra:
             errors.append(f"{path}: unexpected keys {sorted(extra)}.")
-        if not any(k in rule for k in ("sources", "inputs")):
-            errors.append(f"{path}: requires sources or inputs.")
+        if not any(k in rule for k in ("sources", "inputs", "const", "ref")):
+            errors.append(f"{path}: requires sources, inputs, const, or ref.")
         if "sources" in rule:
             _validate_sources(rule["sources"], path, errors)
         if "inputs" in rule:
             _validate_inputs(rule["inputs"], path, errors)
+        if "ref" in rule and not isinstance(rule["ref"], str):
+            errors.append(f"{path}: ref must be a string.")
         if "transform" in rule:
             t = rule["transform"]
             if isinstance(t, list):
@@ -230,11 +232,25 @@ def _validate_map_minimal(map_data: Any) -> List[str]:
     return errors
 
 
-def _validate_map_rule(rule: Any, key: str, errors: List[str], *, idx: Optional[int]) -> None:
+def _validate_map_rule(
+    rule: Any,
+    key: str,
+    errors: List[str],
+    *,
+    idx: Optional[Union[int, str]],
+) -> None:
     label = f"map[{key!r}]" if idx is None else f"map[{key!r}][{idx}]"
     if not isinstance(rule, dict):
         errors.append(f"{label}: rule must be a mapping.")
         return
+    cases = rule.get("cases")
+    if cases is not None:
+        if not isinstance(cases, list):
+            errors.append(f"{label}: cases must be a list.")
+        else:
+            for case_idx, case in enumerate(cases):
+                nested = f"{idx}.cases[{case_idx}]" if idx is not None else f"cases[{case_idx}]"
+                _validate_map_rule(case, key, errors, idx=nested)
     rule_type = rule.get("type")
     if rule_type is None:
         if "values" in rule:
@@ -245,7 +261,7 @@ def _validate_map_rule(rule: Any, key: str, errors: List[str], *, idx: Optional[
         errors.append(f"{label}: invalid type {rule_type!r}.")
     if rule_type == "mapping":
         table = rule.get("values")
-        if not isinstance(table, dict):
+        if not isinstance(table, dict) and cases is None:
             errors.append(f"{label}: values must be a mapping.")
     when = rule.get("when")
     if when is not None and not isinstance(when, dict):

{brkraw-0.5.0rc1.dist-info → brkraw-0.5.1.dist-info}/METADATA

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: brkraw
-Version: 0.5.0rc1
+Version: 0.5.1
 Summary: Toolkit for loading Bruker Paravision datasets, mapping metadata, and exporting NIfTI
 Project-URL: Homepage, https://brkraw.github.io
 Maintainer-email: SungHo Lee <shlee@unc.edu>
 License: GNLv3
 License-File: LICENSE
 Keywords: bruker,cli,conversion,dataset,mri,neuroimaging,nifti,paravision,preclinical
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Natural Language :: English
@@ -44,11 +44,38 @@ Description-Content-Type: text/markdown
 </picture>
 <!-- markdownlint-enable MD041 MD033 MD013 -->
 
-A modular toolkit for preclinical MRI: from raw studies to reproducible outputs.
+[![DOI](https://zenodo.org/badge/245546149.svg)](https://doi.org/10.5281/zenodo.3818614)
 
-BrkRaw (v0.5.0rc1) converts raw data into standardized, neuroimaging-ready
+A modular toolkit for Bruker MRI raw-data handling.
+
+BrkRaw (v0.5.1) converts raw data into standardized, neuroimaging-ready
 datasets, with extensible rules/specs and plugin hooks.
 
 - Documentation: [brkraw.github.io](https://brkraw.github.io/)
 - Releases: [BrkRaw/brkraw releases](https://github.com/BrkRaw/brkraw/releases)
 - PyPI: [brkraw on PyPI](https://pypi.org/project/brkraw/)
+
+## Citation
+
+If you use BrkRaw in your research, please cite it.
+
+- Citation metadata: [CITATION.cff](./CITATION.cff)
+- DOI (Zenodo): [10.5281/zenodo.3818614](https://doi.org/10.5281/zenodo.3818614)
+
+### Cite as (BibTeX)
+
+<!-- BEGIN: brkraw-bibtex -->
+```biblatex
+@software{brkraw_2026,
+  author = {Lee, Sung-Ho and Devenyi, Gabriel A and Ban, Woomi and Shih, Yen-Yu Ian},
+  title = {BrkRaw: A modular toolkit for Bruker MRI raw-data handling},
+  year = {2026},
+  version = {0.5.0},
+  doi = {10.5281/zenodo.3818614},
+  url = {https://github.com/BrkRaw/brkraw},
+  note = {Documentation: https://brkraw.github.io},
+  license = {GPL-3.0-only},
+  date = {2026-01-13}
+}
+```
+<!-- END: brkraw-bibtex -->

{brkraw-0.5.0rc1.dist-info → brkraw-0.5.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-brkraw/__init__.py,sha256=RABNSnaEeMIR7uEFu_8y-fnWcr5sWbz67mDhDH6gXOY,213
+brkraw/__init__.py,sha256=xRDzaw80M_f5rceXUn0qFpdFc04QizjLqQ4XnZjM1iw,210
 brkraw/apps/__init__.py,sha256=sEdA1SrY-Vu0xU1ct5Eab7vX-_IFMDip2j3FdSQVT58,170
 brkraw/apps/addon/__init__.py,sha256=fUR1QNwiaqSbkMIkPxLjKC7mJifR6HhrM8TO7lTo7Mg,531
 brkraw/apps/addon/core.py,sha256=xVlTElgOHNnoy3avNoeOudOvQSDzvuVsmGq9IVKNINc,659
@@ -6,38 +6,39 @@ brkraw/apps/addon/dependencies.py,sha256=Hhujlqmy3DdlLfAM250r3kcl9iX2Lj4eDHBCw0T
 brkraw/apps/addon/installation.py,sha256=LeciuHv_5ENg3OjzKClgIMAg3mYs8h3VUvFXmX6_Nao,18144
 brkraw/apps/addon/io.py,sha256=bjgwl0T1tsL02aAJtScLw3fnh2PfOlmK5aGAQj6WF8Y,413
 brkraw/apps/hook/__init__.py,sha256=W3xf6VmPZkVtQMwnYIrl626fnlck6bO20St0C45tMNY,398
-brkraw/apps/hook/core.py,sha256=PkfhYtltZxRa2zRvj_nE8UCUjbJtBktSrxIxyXFBLE8,18906
+brkraw/apps/hook/core.py,sha256=z6PpwHYYESJD8EO__qVsXZj31YqP5JSSmNHYVHZRCnk,20720
 brkraw/apps/loader/__init__.py,sha256=ytG3wTI3mRHxkLkZ3GNYA6LJduplYgUinZBMuJJkeMQ,163
-brkraw/apps/loader/core.py,sha256=DqEDNC8CIloKYCqxIo7yXpt8XNnu5G6Ru38SAnAGeAw,23119
+brkraw/apps/loader/core.py,sha256=hyc7gk-Bl5g5_bMUdnSY99xjjY9YOt3P0o25QIo0zzE,23268
 brkraw/apps/loader/formatter.py,sha256=WWVCVKdZl6vdyKPCW6rLRmwKuF1cCTTNMPP0vmyBF6Y,9341
-brkraw/apps/loader/helper.py,sha256=yu3mOIRrJn4Yp1bzcrfmTwc2UUjsfQMsSBBARMTtP_A,22621
-brkraw/apps/loader/types.py,sha256=p2CcnmpNRgVB5HnqW8Y6AVjg--X4mgdsiEmFsoB_JOw,6685
+brkraw/apps/loader/helper.py,sha256=Vf8nqgH3KBGIf74f52wcnB1rINEVViUM2O4W8FeGmNs,27879
+brkraw/apps/loader/types.py,sha256=F3EXtV5vEYlHvCBRwjlz3iaTaJiSe7CYC6IayP_bbug,6825
 brkraw/apps/loader/info/__init__.py,sha256=1tWVkBakwf3LZK-FwsMrt10fkkdz9cWw1j-Y4Dk6Lio,164
-brkraw/apps/loader/info/scan.py,sha256=CFVSml9bh3FUO6di7l8GGe94Ub0pwBcVQCh-JbsfF6A,2426
+brkraw/apps/loader/info/scan.py,sha256=_oLBG7YlwVUv1vWXBvCZbXQiMvC1ARKCRNTvrAkqO0U,2849
 brkraw/apps/loader/info/scan.yaml,sha256=tYyGRg4t_rf6jGZAT8F0_dUA9MlQeZ5zeOuTNQ2wQM8,1728
 brkraw/apps/loader/info/study.py,sha256=0_5gUlDOd5xsmXaYF9pyhwUKsq3-oCZ5SMvH6RqlPp4,2743
 brkraw/apps/loader/info/study.yaml,sha256=M_wAy-B-4SErZ610KSNiqUW8aotorXkomymMYFdlyJw,3713
 brkraw/apps/loader/info/transform.py,sha256=vHYBvRbgRfLBPr1-NMUijiJ_p7S2iJ-SPuZsV4rEWqI,2577
 brkraw/cli/__init__.py,sha256=Z97T007Iut9FMPWTRa7MDcUhd9uQhhQ0qmRJ1H4owlw,89
+brkraw/cli/hook_args.py,sha256=B2CKdSmZqSoQaBW4SMtjCXLLheDt-NJ1VwgvGp4Mtzw,2625
 brkraw/cli/main.py,sha256=aqfLycTR_3F-uIEmFi62Q1OUxQ_wwlmQfw-lRfCdPgU,2659
 brkraw/cli/utils.py,sha256=Ii14ZqIVqDx-pIrRAtBrL50yzfEQcQZRtJSRWZ211mE,1348
 brkraw/cli/commands/__init__.py,sha256=PHh4jqD7i0aL8W8hXThczKcT4xsNZiXanBxOH5IOW5I,36
 brkraw/cli/commands/addon.py,sha256=yUK30gQ0AGse1WDifW5DLUCg84RlWGemid0uNVOnxzU,11179
 brkraw/cli/commands/config.py,sha256=bcbLQpb7Vw_imYwQsds4ZbWAOtgj_Dw3ojmFN4UmMBs,6471
-brkraw/cli/commands/convert.py,sha256=m_Yvqodqsf5K5UXiAhtMcPnTdUGRXlrqgvgovbtXfJ8,25487
-brkraw/cli/commands/hook.py,sha256=TSgaIfzOkTCzzrM_YhfWDAvAJGysVXX7onvKEdgL6ig,7306
+brkraw/cli/commands/convert.py,sha256=8mkJYZCFXKahqqOIN_C4W7F_qbcwR0idYy40cdhZILU,30615
+brkraw/cli/commands/hook.py,sha256=nPGIVMlWrpIJDCMdJABKGzV4HcuBdC3bLIh8cqJ8He4,11925
 brkraw/cli/commands/info.py,sha256=fwojS5GlEf2upY3v5-ueQQQf9CPWTn46-1-tub2gnxQ,2251
 brkraw/cli/commands/init.py,sha256=FLOimOmZbkrCRjTm0iJ8_w8o027He5dzbl3UT2Zu72U,6957
 brkraw/cli/commands/params.py,sha256=5z_2O24IrUL-_AEjHIzjZHA_89piDHtXkxHkd7C12D0,3159
 brkraw/cli/commands/prune.py,sha256=Sl8Zl78PAGtRvDB6HH-CqcDr4NBfXSrf8602ZAKL7nM,8798
-brkraw/cli/commands/session.py,sha256=GRlK3sdoxrHzznPMTDDDrnsNGJqpLv9ypwlO2ribtjo,12488
+brkraw/cli/commands/session.py,sha256=COEjRwy-Z-Y9_-SZVAwUsIpDutXQ0UQ1baMNvjN6jYU,12749
 brkraw/core/__init__.py,sha256=9UPOF5mtjZdGgjQ6-JJJs-eg8CGl4BuV7flGDWKgCBg,218
-brkraw/core/config.py,sha256=g8wg58wsTxSP0Lwk1i4Jx7Lm1lA6_8nbMZTzCGgSLsY,11556
+brkraw/core/config.py,sha256=fohxJOoBruBrdzFIrXmBmZE5AW9EpnTOLAr3am8xDM8,11820
 brkraw/core/entrypoints.py,sha256=OqEvqBna7fTjR8MofIGJE80EzxL0WUYxeiJEUlQjfR8,880
 brkraw/core/formatter.py,sha256=5OcJOkQ3mcoRqt6SPib01fA5riObL1wbiJL4rsNwFEw,11387
 brkraw/core/fs.py,sha256=IMhdguizZEcrpcx9eb41MKJnfMoLuvoWDhVmV83mW9M,17337
 brkraw/core/jcamp.py,sha256=TaI-SrhoAA1tXpiVzVqn83NV0OHxTO0tAf_k1YXIWFE,17626
-brkraw/core/layout.py,sha256=_ulaH2m6ZdU1r_Y6s1u7vazMcs-WOqsoMi562C6LsHY,13118
+brkraw/core/layout.py,sha256=F69Wglkp-3M7LNP3162cU17rWcQ7MSYenFSvXgyJUGY,14253
 brkraw/core/parameters.py,sha256=_Nl7K0yT149tm0c2SXQbYWhZD5z29ySbZPc78d7zOU8,27983
 brkraw/core/zip.py,sha256=m0mixVf4bb116QzAF_3o6-3EDCeq53JhjfKq0NLl5K0,37805
 brkraw/dataclasses/__init__.py,sha256=cAYJ_XqyHtpK9OaLaXsjwySbWuIkznrTGa68OnKZFxs,211
@@ -47,16 +48,11 @@ brkraw/dataclasses/scan.py,sha256=VjmT8depuYJzeI4E2sduut-cLZiqf_fIUe06wbvW108,19
 brkraw/dataclasses/study.py,sha256=2qGDDQQgJMHDENVCug_iJ5fUwGLhVhRLwrbgzP60r0g,4540
 brkraw/default/__init__.py,sha256=eEYYkxX5Hz9woXVOBJ2H2_CQoEih0vH6nRt3sH2Z8v8,49
 brkraw/default/pruner_specs/deid4share.yaml,sha256=TnQrlF9GGub5wiJ81SQOXALvLfJWHynxY-ZoQ8y_oZs,949
-brkraw/default/rules/10-metadata.yaml,sha256=dceK8nr-4o8v_n41RuH3py7V6G0aX0d7o3jmr1TDNZA,1109
-brkraw/default/rules/20-mrs.yaml,sha256=IghyjQV6YLnXiysa9WqO5hFsoCrPr2R2JPOUxHLIi5c,364
-brkraw/default/specs/metadata_anat.yaml,sha256=1JBxAFGbuON2OlFRcZg99LJBfVu141Z0pJ4qeRDwrqQ,912
-brkraw/default/specs/metadata_common.yaml,sha256=pDcwHa-f2d2v9X_3UHmwoYkiHNFkxThyEZUyzPUrIxQ,2443
-brkraw/default/specs/metadata_func.yaml,sha256=IK8f5zRmopxqyRKgkAHj6sqDjfm7plKQ5Q9mTLpFJoI,2059
-brkraw/default/specs/metadata_transforms.py,sha256=mfb9ogfxd0VzZmxmXf57AK2iGIrktTnMWakiLKSVCkk,1745
-brkraw/default/specs/mrs.yaml,sha256=7r0CXTe6pBxrmTqg2JCjamwPTSDepfHj37T28z8jG1o,1246
-brkraw/default/specs/mrs_transforms.py,sha256=3dxfv1-yfnowOWCacXp2Ucy7tc_MpgxMn2Hh4MVPSSQ,622
+brkraw/default/rules/00_default.yaml,sha256=a4PZOR0oam0ziZqLsvaQZqwoDu-uXbPVdxJcm9rSy0o,140
+brkraw/default/specs/metadata_dicom.yaml,sha256=grrwGOBIIEUJPTs6vktWydnEsvBTjbgwez0190Q8ma0,4295
+brkraw/default/specs/metadata_transforms.py,sha256=illM4MKwwz-6PPKLrIno5lba1f5zKC8y09PAR5gCH1o,2383
 brkraw/resolver/__init__.py,sha256=2vz8b135CA4aebHUHSc2Hgtc3Ko2-qbdAxfTnUtTeGk,84
-brkraw/resolver/affine.py,sha256=V-UggK8sV8b4M0ODdu1Z0ohrViVM_rJ2CqI4n42Ahp8,18333
+brkraw/resolver/affine.py,sha256=s7vm30C5fkmOMTuY-Bc5lZeE3Wy4pbHydL1V4gzkDB4,19501
 brkraw/resolver/datatype.py,sha256=Kp-_-_JDfCh4io19Vw4YiAVTjWgaFAkxkO7ZDDglAKY,2155
 brkraw/resolver/fid.py,sha256=SXglNSD6hFK7pAoHrUvuNbCYPgIAvbRdh6PACp7Oz7g,2847
 brkraw/resolver/helpers.py,sha256=BpL-zpbtGae6n-XQOmD5qP7KrD5HFnElzAD3bcBq0J4,1029
@@ -64,29 +60,29 @@ brkraw/resolver/image.py,sha256=01mqBVFfoY2Z0V60k3G0qTKpEH-lqRCaSdkZ7pj7Bb8,6735
 brkraw/resolver/nifti.py,sha256=otqjDeRZMpplC6Z_uxWMjKoNtxvQyELvwK-ZbVMTuf8,12870
 brkraw/resolver/shape.py,sha256=r2sQpgKGMN0nmBPj9_LTt7d3ls-y4R8n1HIMDvpNdfk,8110
 brkraw/schema/__init__.py,sha256=eEYYkxX5Hz9woXVOBJ2H2_CQoEih0vH6nRt3sH2Z8v8,49
-brkraw/schema/context_map.yaml,sha256=9Bw7RLHsSETVamR-a2VIgsW4XP4BHeYOYrl2of4IfBg,1638
+brkraw/schema/context_map.yaml,sha256=OUtoa7NgQZ7ytUe8zuNiJ5ratt1p0DRrrfDAP5Kthqs,1798
 brkraw/schema/meta.yaml,sha256=ePnTt7jD00lMKob6MPoziws9eYOWa-BX2MrVrIMSo90,1042
 brkraw/schema/niftiheader.yaml,sha256=Hj7eQNyLbyuT__-jznzAB15JIP9ArRhBGvJstZFGNZg,1499
 brkraw/schema/pruner.yaml,sha256=bTmxvs5naAt_CsPQC-nIUEF5aL2T-iWUWGhg05ug_Ic,1023
-brkraw/schema/remapper.yaml,sha256=TPSf94AAlN3PteFkOxVPkwwsvmic92zx-drx4v46wpU,3449
+brkraw/schema/remapper.yaml,sha256=qIGiT6DqrJ2AK8g7gHj7Cc6GmQIT47VPaB2nRvnNc8k,3622
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 brkraw/specs/pruner/logic.py,sha256=c6mSST6yTgwJD75ORI-G4EtC4Txgbdhu-P0xdzjsxMA,13070
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 brkraw/specs/rules/__init__.py,sha256=oF1ury9vxTYMlTgz9Yo9um8jRAzaJeTMwjAcDLV-KOE,214
 brkraw/specs/rules/logic.py,sha256=w-NstF6o91EfLU2Ho00i8kbvvd7d8yrinPd83UnAW2c,9175
 brkraw/specs/rules/validator.py,sha256=AHS-r-E0HGHxwhhU48nCyS6LQvllQCgXLS_NDXBm3-k,3508
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brkraw/default/rules/10-metadata.yaml

@@ -1,42 +0,0 @@
-metadata_spec:
-  - name: "metadata-common"
-    description: "Default metadata mapping for Bruker scans."
-    use: "specs/metadata_common.yaml"
-
-  - name: "metadata-anat"
-    description: "Anatomical metadata mapping for RARE/FLASH sequences."
-    when:
-      method:
-        sources:
-          - file: method
-            key: Method
-        transform: normalize_method
-    if:
-      any:
-        - contains: ["$method", "RARE"]
-        - contains: ["$method", "FLASH"]
-    use: "specs/metadata_anat.yaml"
-
-  - name: "metadata-func-epi"
-    description: "Functional metadata mapping for EPI with short TR."
-    when:
-      method:
-        sources:
-          - file: method
-            key: Method
-        transform: normalize_method
-      tr_sec:
-        sources:
-          - file: method
-            key: PVM_RepetitionTime
-        transform: first_seconds
-      num_repeats:
-        sources:
-          - file: method
-            key: PVM_NRepetitions
-    if:
-      all:
-        - contains: ["$method", "EPI"]
-        - le: ["$tr_sec", 4]
-        - gt: ["$num_repeats", 5]
-    use: "specs/metadata_func.yaml"

brkraw/default/rules/20-mrs.yaml

@@ -1,14 +0,0 @@
-info_spec:
-  - name: "mrs-method"
-    description: "Use MRS info spec for PRESS/STEAM/SLASER sequences."
-    when:
-      method:
-        sources:
-          - file: method
-            key: Method
-    if:
-      any:
-        - contains: ["$method", "PRESS"]
-        - contains: ["$method", "STEAM"]
-        - contains: ["$method", "SLASER"]
-    use: "specs/mrs.yaml"

brkraw/default/specs/metadata_anat.yaml

@@ -1,54 +0,0 @@
-__meta__:
-  name: "metadata_anat"
-  version: "0.0.1"
-  description: "Anatomical metadata mapping for BIDS 1.10.1."
-  category: "metadata_spec"
-  include:
-    - "metadata_common.yaml"
-
-RepetitionTime:
-  sources:
-    - file: visu_pars
-      key: VisuAcqRepetitionTime
-  transform: to_seconds
-
-EchoTime:
-  sources:
-    - file: visu_pars
-      key: VisuAcqEchoTime
-  transform: to_seconds
-
-InversionTime:
-  sources:
-    - file: visu_pars
-      key: VisuAcqInversionTime
-  transform: to_seconds
-
-FlipAngle:
-  sources:
-    - file: visu_pars
-      key: VisuAcqFlipAngle
-
-PhaseEncodingDirection:
-  inputs:
-    value:
-      const: null
-  transform: pick_value
-
-EffectiveEchoSpacing:
-  inputs:
-    value:
-      const: null
-  transform: pick_value
-
-TotalReadoutTime:
-  inputs:
-    value:
-      const: null
-  transform: pick_value
-
-MultibandAccelerationFactor:
-  inputs:
-    value:
-      const: null
-  transform: pick_value

brkraw/default/specs/metadata_common.yaml

@@ -1,129 +0,0 @@
-__meta__:
-  name: "metadata_common"
-  version: "0.0.1"
-  description: "Common BIDS 1.10.1 metadata mapping for Bruker PvDataset."
-  category: "metadata_spec"
-  transforms_source: "metadata_transforms.py"
-
-Manufacturer:
-  sources:
-    - file: visu_pars
-      key: VisuManufacturer
-  transform: strip_jcamp_string
-
-ManufacturersModelName:
-  sources:
-    - file: visu_pars
-      key: VisuStation
-  transform: strip_jcamp_string
-
-DeviceSerialNumber:
-  sources:
-    - file: visu_pars
-      key: VisuSystemOrderNumber
-
-StationName:
-  sources:
-    - file: visu_pars
-      key: VisuStation
-  transform: strip_jcamp_string
-
-SoftwareVersions:
-  sources:
-    - file: visu_pars
-      key: VisuAcqSoftwareVersion
-  transform: strip_jcamp_string
-
-MagneticFieldStrength:
-  inputs:
-    freq:
-      sources:
-        - file: visu_pars
-          key: VisuAcqImagingFrequency
-  transform: freq_to_field
-
-ReceiveCoilName:
-  sources:
-    - file: visu_pars
-      key: VisuCoilReceiveName
-  transform: strip_jcamp_string
-
-ReceiveCoilActiveElements:
-  sources:
-    - file: visu_pars
-      key: VisuCoilReceiveType
-  transform: strip_jcamp_string
-
-TransmitCoilName:
-  sources:
-    - file: visu_pars
-      key: VisuCoilTransmitName
-  transform: strip_jcamp_string
-
-CoilCombinationMethod:
-  inputs:
-    value:
-      const: null
-  transform: pick_value
-
-GradientSetType:
-  sources:
-    - file: acqp
-      key: ACQ_status
-  transform: strip_jcamp_string
-
-PulseSequenceType:
-  sources:
-    - file: method
-      key: PULPROG
-  transform: strip_jcamp_string
-
-ScanningSequence:
-  sources:
-    - file: visu_pars
-      key: VisuAcqSequenceName
-  transform: strip_jcamp_string
-
-SequenceVariant:
-  sources:
-    - file: visu_pars
-      key: VisuAcqEchoSequenceType
-  transform: strip_jcamp_string
-
-SequenceName:
-  sources:
-    - file: visu_pars
-      key: VisuAcquisitionProtocol
-    - file: acqp
-      key: ACQ_protocol_name
-  transform: strip_jcamp_string
-
-PulseSequenceDetails:
-  sources:
-    - file: acqp
-      key: ACQ_scan_name
-  transform: strip_jcamp_string
-
-NonlinearGradientCorrection:
-  sources:
-    - file: visu_pars
-      key: VisuAcqKSpaceTraversal
-  transform: strip_jcamp_string
-
-InstitutionName:
-  sources:
-    - file: visu_pars
-      key: VisuInstitution
-  transform: strip_jcamp_string
-
-InstitutionAddress:
-  inputs:
-    value:
-      const: null
-  transform: pick_value
-
-InstitutionalDepartmentName:
-  inputs:
-    value:
-      const: null
-  transform: pick_value