Read the PROCNO spectroscopy fids as interleaved float64

brukerapi/config/properties_fid_proc_core.json

@@ -0,0 +1,44 @@
+{
+  "pv_version": [
+    {
+      "cmd": "(#ACQ_sw_version).replace('PV-','').replace('PV ','').strip()",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "numpy_dtype": [
+    {
+      "cmd": "np.dtype('f8').newbyteorder('>' if #BYTORDA=='big' else '<')",
+      "conditions": [],
+      "comment": "spec 3.5: fid_proc.64 / fid_refscan.64 hold 64-bit doubles, whatever the raw acquisition word type is. The .64 suffix is the word size"
+    }
+  ],
+  "shape_final": [
+    {
+      "cmd": "(int(np.prod(np.atleast_1d(#PVM_SpecMatrix))),)",
+      "conditions": [],
+      "comment": "spec 3.5: one complex float64 pair per spectral point, so the file is 8 * 2 * PVM_SpecMatrix bytes"
+    },
+    {
+      "cmd": "(int(file_size(self.path) // @numpy_dtype.itemsize // 2),)",
+      "conditions": [],
+      "comment": "PVM_SpecMatrix is a method parameter and need not be there; fall back on the file itself"
+    }
+  ],
+  "shape_storage": [
+    {
+      "cmd": "(2 * @shape_final[0],)",
+      "conditions": [],
+      "comment": "real and imaginary interleaved"
+    }
+  ],
+  "dim_type": [
+    {
+      "cmd": ["'k_space_encode_step_0'"],
+      "conditions": []
+    }
+  ]
+}

brukerapi/config/properties_fid_proc_custom.json

@@ -0,0 +1,63 @@
+{
+  "subj_id": [
+    {
+      "cmd": "#SUBJECT_id",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "study_id": [
+    {
+      "cmd": "str(#SUBJECT_study_nr)",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "exp_id": [
+    {
+      "cmd": "@path.parents[2].name",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "proc_id": [
+    {
+      "cmd": "@path.parents[0].name",
+      "conditions": []
+    },
+    {
+      "cmd": "''",
+      "conditions": []
+    }
+  ],
+  "id": [
+    {
+      "cmd": "'{}_{}_{}_{}_{}'.format(@type.upper(), @exp_id, @proc_id, @subj_id, @study_id)",
+      "conditions": [],
+      "comment": "spec 3.5: these live in the PROCNO, so the id names the reconstruction as a 2dseq id does"
+    }
+  ],
+  "TE": [
+    {
+      "cmd": "#PVM_EchoTime",
+      "conditions": [],
+      "unit": "ms"
+    }
+  ],
+  "TR": [
+    {
+      "cmd": "#PVM_RepetitionTime",
+      "conditions": [],
+      "unit": "ms"
+    }
+  ]
+}

brukerapi/dataset.py

@@ -63,9 +63,18 @@
         "load": LOAD_STAGES["all"],
         "mmap": False,
     },
+    # Spec 3.5: the PV360 spectroscopy PROCNO files, 64-bit doubles with real and
+    # imaginary interleaved -- not the acquisition word type, and not the fid
+    # block model, so they get recipes of their own.
     "fid_proc": {
         "parameter_files": ["acqp", "method"],
-        "property_files": [Path(__file__).parents[0] / "config/properties_fid_core.json", Path(__file__).parents[0] / "config/properties_fid_custom.json"],
+        "property_files": [Path(__file__).parents[0] / "config/properties_fid_proc_core.json", Path(__file__).parents[0] / "config/properties_fid_proc_custom.json"],
+        "load": LOAD_STAGES["all"],
+        "mmap": False,
+    },
+    "fid_refscan": {
+        "parameter_files": ["acqp", "method"],
+        "property_files": [Path(__file__).parents[0] / "config/properties_fid_proc_core.json", Path(__file__).parents[0] / "config/properties_fid_proc_custom.json"],
         "load": LOAD_STAGES["all"],
         "mmap": False,
     },
@@ -116,6 +125,18 @@
         "AdjStatePerScan": "../../AdjStatePerScan",
         "AdjStatePerStudy": "../../../AdjStatePerStudy",
     },
+    "fid_refscan": {
+        "method": "../../method",
+        "acqp": "../../acqp",
+        "subject": "../../../subject",
+        "reco": "./reco",
+        "methreco": "./methreco",
+        "pvmeta": "./pvmeta",
+        "d3proc": "./d3proc",
+        "visu_pars": "./visu_pars",
+        "AdjStatePerScan": "../../AdjStatePerScan",
+        "AdjStatePerStudy": "../../../AdjStatePerStudy",
+    },
     "2dseq": {
         "method": "../../method",
         "acqp": "../../acqp",
@@ -174,6 +195,7 @@
 SUPPORTED_SUBTYPES = {
     "fid": {""},
     "fid_proc": {"64"},
+    "fid_refscan": {"64"},
     "2dseq": {""},
     "traj": {""},
     "rawdata": {"Navigator"},
@@ -245,11 +267,7 @@ def __init__(self, path, **state):
                 (name for name in content if re.fullmatch(r"rawdata\.job\d+", name)),
                 key=lambda name: int(name.rsplit("job", 1)[1]),
             )
-            named_rawdata_jobs = sorted(
-                name
-                for name in content
-                if name not in rawdata_jobs and self.is_supported_path(self.path / name, {"rawdata"})
-            )
+            named_rawdata_jobs = sorted(name for name in content if name not in rawdata_jobs and self.is_supported_path(self.path / name, {"rawdata"}))
             if "fid" in content:
                 self.path = self.path / "fid"
             elif "2dseq" in content:
@@ -273,10 +291,7 @@ def __init__(self, path, **state):
         if self.type not in DEFAULT_STATES:
             raise UnsupportedDatasetType(self.type)
         if self.type == "fid" and self.subtype in FID_COMPANION_SUBTYPES and not state.get("_auxiliary"):
-            raise UnsupportedDatasetType(
-                f"{self.path.name} is a fid companion (spec §3.5); load it as "
-                f"Dataset({with_suffix(self.path, '')!s}).fid_companions[{self.subtype!r}]"
-            )
+            raise UnsupportedDatasetType(f"{self.path.name} is a fid companion (spec §3.5); load it as Dataset({with_suffix(self.path, '')!s}).fid_companions[{self.subtype!r}]")
         if not self._is_supported_subtype() and not (state.get("_auxiliary") and self.type == "fid" and self.subtype in FID_COMPANION_SUBTYPES):
             raise UnsupportedDatasetType(self.path.name)
 
@@ -529,7 +544,7 @@ def _read_parameters(self):
         reco_path = self._state.get("reco_path")
         if reco_path is not None:
             self.add_parameter_file(reco_path)
-        elif self.type in {"fid", "fid_proc"}:
+        elif self.type == "fid":
             with suppress(FileNotFoundError):
                 self.add_parameter_file("reco")
 
@@ -596,9 +611,9 @@ def get(self, name, default=None):
         A name no configuration declares still raises, so a typo does not
         quietly become `default`::
 
-            dataset.get("TE")           # 4.0, or None where there is no echo time
-            dataset.get("TE", "n/a")    # 4.0, or "n/a"
-            dataset.get("TEE")          # AttributeError
+            dataset.get("TE")  # 4.0, or None where there is no echo time
+            dataset.get("TE", "n/a")  # 4.0, or "n/a"
+            dataset.get("TEE")  # AttributeError
 
         Parameters are a separate layer, read with ``dataset[key]`` or
         ``dataset.parameters``.
@@ -727,8 +742,7 @@ def rawdata_stored_scans(self):
         settings_stored = int(settings[9])
         if settings_stored != job_stored and not getattr(self, "_warned_rawdata_stored_scans", False):
             warnings.warn(
-                f"ACQ_ScanPipeJobSettings nStoredScans={settings_stored} disagrees with "
-                f"ACQ_jobs nStoredScans={job_stored} for {self.path}; using the settings value",
+                f"ACQ_ScanPipeJobSettings nStoredScans={settings_stored} disagrees with ACQ_jobs nStoredScans={job_stored} for {self.path}; using the settings value",
                 RuntimeWarning,
                 stacklevel=2,
             )
@@ -779,9 +793,7 @@ def _infer_scheme_id(self):
         if descriptions and descriptions[0] == "Spectroscopic":
             return "SPECTROSCOPY" if int(dim) == 1 else "CSI"
 
-        if n_projections is not None and int(n_projections) > 0 and (
-            (self.path.parent / "traj").exists() or "RADIAL" in family or "UTE" in family
-        ):
+        if n_projections is not None and int(n_projections) > 0 and ((self.path.parent / "traj").exists() or "RADIAL" in family or "UTE" in family):
             return "RADIAL"
 
         acq_size = np.atleast_1d(self._parameter_value("ACQ_size", []))
@@ -860,8 +872,10 @@ def load_schema(self):
         """
         Load the schema for given data set.
         """
-        if self.type in ["fid", "fid_proc"]:
+        if self.type == "fid":
             self._schema = SchemaFid(self)
+        elif self.type in {"fid_proc", "fid_refscan"}:
+            self._schema = SchemaFidCompanion(self)
         elif self.type == "2dseq":
             self._schema = Schema2dseq(self)
         elif self.type == "rawdata":
@@ -940,9 +954,7 @@ def _read_binary_file(self, path, dtype, shape):
                     f"expected {expected_bytes} bytes for shape {tuple(shape)} and dtype {dtype}"
                 )
 
-            raise InvalidDataset(
-                f"Invalid dataset size at {path}: expected {expected_bytes} bytes for shape {tuple(shape)} and dtype {dtype}, got {actual_bytes} bytes"
-            )
+            raise InvalidDataset(f"Invalid dataset size at {path}: expected {expected_bytes} bytes for shape {tuple(shape)} and dtype {dtype}, got {actual_bytes} bytes")
 
         return read_array(path, dtype, shape)
 
@@ -1343,9 +1355,7 @@ def affine(self):
         """
         descriptors = np.atleast_1d(np.asarray(self._parameter_value("VisuCoreDimDesc", []))).astype(str)
         if descriptors.size and any(descriptor != "spatial" for descriptor in descriptors):
-            raise UnsupportedDatasetType(
-                f"an image affine for {self.path}, whose frames are {sorted(set(descriptors))} rather than purely spatial (spec 7.2),"
-            )
+            raise UnsupportedDatasetType(f"an image affine for {self.path}, whose frames are {sorted(set(descriptors))} rather than purely spatial (spec 7.2),")
         if len(self.slice_packages_index()) > 1:
             warnings.warn(
                 f"{self.path} has multiple slice packages; a single affine cannot describe them -- use get_slice_packages() / affine_of_package(i)",
@@ -1405,7 +1415,7 @@ def to_kspace(self, *, bart=False):
         API: EPI and non-Cartesian raw data require acquisition-specific
         handling.
         """
-        if self.type not in {"fid", "fid_proc", "rawdata"}:
+        if self.type not in {"fid", "rawdata"}:
             raise UnsupportedDatasetType(f"k-space conversion is not available for {self.type} datasets")
         return self._schema.to_kspace(bart=bart)