Slice-package splitting requires VisuCoreSlicePacksSlices, which PV5.…

brukerapi/config/properties_2dseq_core.json

@@ -161,14 +161,9 @@
   ],
   "num_slice_packages": [
       {
-        "cmd": "len(#VisuCoreSlicePacksSlices.nested)",
-        "conditions": []
-      },
-      {
-        "cmd": "1",
+        "cmd": "len(@slice_packages_index())",
         "conditions": []
       }
-
   ],
   "slope": [
     {

brukerapi/dataset.py

@@ -1204,7 +1204,7 @@ def get_slice_packages(self):
         """
         if self.type != "2dseq":
             raise UnsupportedDatasetType(f"slice packages are only available for 2dseq, not {self.type}")
-        if self.num_slice_packages <= 1:
+        if len(self.slice_packages_index()) <= 1:
             return [self]
 
         from .splitters import SlicePackageSplitter

brukerapi/splitters.py

@@ -4,7 +4,7 @@
 import numpy as np
 
 from .dataset import Dataset
-from .exceptions import MissingProperty
+from .jcampdx import JCAMPDX
 from .utils import index_to_slice
 
 SUPPORTED_FG = ["FG_ISA", "FG_IRMODE", "FG_ECHO"]
@@ -286,17 +286,11 @@ def split(self, dataset, write=None, path_out=None):
         if write is None:
             write = False
 
-        try:
-            VisuCoreSlicePacksSlices = dataset["VisuCoreSlicePacksSlices"].nested
-        except KeyError:
-            raise MissingProperty("Parameter VisuCoreSlicePacksSlices not found") from KeyError
+        packages = dataset.slice_packages_index()
 
         # list of split data sets
         datasets = []
 
-        # range of frames of given slice package
-        frame_range = range(0, 0)
-
         # Which frame group holds the slices. Spec 7.10: VisuCoreSlicePacksDef is
         # (fg_index, num_packages), and an fg_index of -1 is a documented sentinel
         # meaning there is no slices frame group and every frame belongs to the
@@ -313,12 +307,8 @@ def split(self, dataset, write=None, path_out=None):
         fg_abs_index = fg_rel_index + dataset.encoded_dim
 
         # slice package split loop
-        for sp_index in range(len(VisuCoreSlicePacksSlices)):
-            # set range
-            frame_range = range(frame_range.stop, frame_range.stop + VisuCoreSlicePacksSlices[sp_index][1])
-
-            # number of frames contained in given slice package
-            frame_count = frame_range.stop - frame_range.start
+        for sp_index, (first_frame, frame_count) in enumerate(packages):
+            frame_range = range(first_frame, first_frame + frame_count)
 
             # name of the data set created by the split
             name = f"{dataset.path.parents[0].name}_sp_{sp_index}/2dseq"
@@ -373,9 +363,9 @@ def _split_parameters(self, dataset, frame_range, *, fg_rel_index, fg_abs_index,
             self._split_VisuCoreTransposition(dataset, visu_pars_, frame_range, fg_rel_index)
         self._split_VisuCoreFrameCount(dataset, visu_pars_, frame_count, fg_abs_index)
         self._split_VisuFGOrderDesc(visu_pars_, fg_rel_index, frame_count)
-        self._split_VisuCoreSlicePacksDef(visu_pars_)
-        self._split_VisuCoreSlicePacksSlices(visu_pars_, sp_index)
-        self._split_VisuCoreSlicePacksSliceDist(visu_pars_, sp_index)
+        self._split_VisuCoreSlicePacksDef(visu_pars_, fg_rel_index)
+        self._split_VisuCoreSlicePacksSlices(visu_pars_, frame_count)
+        self._split_VisuCoreSlicePacksSliceDist(dataset, visu_pars_, sp_index)
 
         return {"visu_pars": visu_pars_}
 
@@ -410,18 +400,34 @@ def _split_VisuFGOrderDesc(self, visu_pars, fg_rel_ind, frame_count):
 
         VisuFGOrderDesc.value = value
 
-    def _split_VisuCoreSlicePacksDef(self, visu_pars):
+    @staticmethod
+    def _synthesise_parameter(visu_pars, key, value):
+        _, parameter = JCAMPDX.handle_jcampdx_line(f"##${key}={value}", visu_pars.version)
+        visu_pars.set_parameter(key, parameter)
+
+    def _split_VisuCoreSlicePacksDef(self, visu_pars, fg_rel_index):
+        if "VisuCoreSlicePacksDef" not in visu_pars:
+            self._synthesise_parameter(visu_pars, "VisuCoreSlicePacksDef", f"({fg_rel_index}, 1)")
+            return
         VisuCoreSlicePacksDef = visu_pars["VisuCoreSlicePacksDef"]
         value = VisuCoreSlicePacksDef.value
         value[1] = 1
         VisuCoreSlicePacksDef.value = value
 
-    def _split_VisuCoreSlicePacksSlices(self, visu_pars_, sp_index):
-        VisuCoreSlicePacksSlices = visu_pars_["VisuCoreSlicePacksSlices"]
-        VisuCoreSlicePacksSlices.value = [VisuCoreSlicePacksSlices.value[sp_index]]
-
-    def _split_VisuCoreSlicePacksSliceDist(self, visu_pars_, sp_index):
-        VisuCoreSlicePacksSliceDist = visu_pars_["VisuCoreSlicePacksSliceDist"]
+    def _split_VisuCoreSlicePacksSlices(self, visu_pars, frame_count):
+        if "VisuCoreSlicePacksSlices" not in visu_pars:
+            self._synthesise_parameter(visu_pars, "VisuCoreSlicePacksSlices", f"( 1 )\n(0, {frame_count})")
+            return
+        VisuCoreSlicePacksSlices = visu_pars["VisuCoreSlicePacksSlices"]
+        VisuCoreSlicePacksSlices.value = [[0, frame_count]]
+        VisuCoreSlicePacksSlices.size = (1,)
+
+    def _split_VisuCoreSlicePacksSliceDist(self, dataset, visu_pars, sp_index):
+        if "VisuCoreSlicePacksSliceDist" not in visu_pars:
+            distance = float(np.linalg.norm(dataset.affine_of_package(sp_index)[:3, 2]))
+            self._synthesise_parameter(visu_pars, "VisuCoreSlicePacksSliceDist", str(distance))
+            return
+        VisuCoreSlicePacksSliceDist = visu_pars["VisuCoreSlicePacksSliceDist"]
         # spec 7.10: the inter-slice distance is a double, and truncating it
         # loses the fractional millimetres of every non-integer slice spacing
         value = float(VisuCoreSlicePacksSliceDist.array[sp_index])

test/test_split.py

@@ -4,7 +4,7 @@
 
 from brukerapi.dataset import Dataset
 from brukerapi.splitters import FrameGroupSplitter, SlicePackageSplitter, Splitter
-from test.synthetic import stacked_positions, write_2dseq
+from test.synthetic import axial_orientation, stacked_positions, write_2dseq
 
 
 def test_split_transposition_is_noop_when_parameter_is_absent():
@@ -51,6 +51,35 @@ def test_splitSlicePkg(test_split_data, tmp_path):
     assert len(datasets) == dataset["VisuCoreSlicePacksSlices"].size[0]
 
 
+def test_slice_package_splitter_infers_and_synthesises_pv51_packages(tmp_path):
+    """PV5.1 has no §7.10 package parameters; orientation delimits packages."""
+    sagittal = np.array([0.0, 1.0, 0.0, 0.0, 0.0, 1.0, -1.0, 0.0, 0.0])
+    positions = np.vstack(
+        [
+            stacked_positions((-20.0, -20.0, -3.0), (0.0, 0.0, 1.5), 2),
+            stacked_positions((0.0, -20.0, -20.0), (-1.0, 0.0, 0.0), 3),
+        ]
+    )
+    orientations = np.vstack([axial_orientation(2), np.tile(sagittal, (3, 1))])
+    path = write_2dseq(
+        tmp_path / "9" / "pdata" / "1",
+        creator_version="5.1",
+        frame_groups=(("FG_SLICE", 5),),
+        positions=positions,
+        orientations=orientations,
+    )
+
+    dataset = Dataset(path)
+    packages = SlicePackageSplitter().split(dataset, write=True)
+
+    assert dataset.num_slice_packages == 2
+    assert [package.data.shape[2] for package in packages] == [2, 3]
+    assert all(package.num_slice_packages == 1 for package in packages)
+    assert [package["VisuCoreSlicePacksSlices"].nested for package in packages] == [[[0, 2]], [[0, 3]]]
+    assert [package["VisuCoreSlicePacksDef"].value for package in packages] == [[0, 1], [0, 1]]
+    assert [Dataset(package.path).num_slice_packages for package in packages] == [1, 1]
+
+
 def _echo_dataset(tmp_path, echoes=2, slices=3):
     path = write_2dseq(
         tmp_path / "5" / "pdata" / "1",