IHeader

src/mrpro/data/IHeader.py

@@ -2,45 +2,127 @@
 
 import dataclasses
 from collections.abc import Sequence
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 
-import numpy as np
 import torch
+from einops import repeat
 from pydicom.dataset import Dataset
 from pydicom.tag import Tag, TagType
 from typing_extensions import Self
 
 from mrpro.data.KHeader import KHeader
 from mrpro.data.MoveDataMixin import MoveDataMixin
+from mrpro.data.Rotation import Rotation
 from mrpro.data.SpatialDimension import SpatialDimension
+from mrpro.utils.remove_repeat import remove_repeat
 from mrpro.utils.summarize_tensorvalues import summarize_tensorvalues
+from mrpro.utils.unit_conversion import deg_to_rad, mm_to_m, ms_to_s
+
+from .AcqInfo import PhysiologyTimestamps
 
 MISC_TAGS = {'TimeAfterStart': 0x00191016}
 
 
+def _int_factory() -> torch.Tensor:
+    return torch.zeros(1, 1, dtype=torch.int64)
+
+
+@dataclass(slots=True)
+class ImageIdx(MoveDataMixin):
+    """Acquisition index for each readout."""
+
+    average: torch.Tensor = field(default_factory=_int_factory)
+    """Signal average."""
+
+    slice: torch.Tensor = field(default_factory=_int_factory)
+    """Slice number (multi-slice 2D)."""
+
+    contrast: torch.Tensor = field(default_factory=_int_factory)
+    """Echo number in multi-echo."""
+
+    phase: torch.Tensor = field(default_factory=_int_factory)
+    """Cardiac phase."""
+
+    repetition: torch.Tensor = field(default_factory=_int_factory)
+    """Counter in repeated/dynamic acquisitions."""
+
+    set: torch.Tensor = field(default_factory=_int_factory)
+    """Sets of different preparation, e.g. flow encoding, diffusion weighting."""
+
+    user0: torch.Tensor = field(default_factory=_int_factory)
+    """User index 0."""
+
+    user1: torch.Tensor = field(default_factory=_int_factory)
+    """User index 1."""
+
+    user2: torch.Tensor = field(default_factory=_int_factory)
+    """User index 2."""
+
+    user3: torch.Tensor = field(default_factory=_int_factory)
+    """User index 3."""
+
+    user4: torch.Tensor = field(default_factory=_int_factory)
+    """User index 4."""
+
+    user5: torch.Tensor = field(default_factory=_int_factory)
+    """User index 5."""
+
+    user6: torch.Tensor = field(default_factory=_int_factory)
+    """User index 6."""
+
+    user7: torch.Tensor = field(default_factory=_int_factory)
+    """User index 7."""
+
+
 @dataclass(slots=True)
 class IHeader(MoveDataMixin):
     """MR image data header."""
 
-    # ToDo: decide which attributes to store in the header
     fov: SpatialDimension[float]
     """Field of view [m]."""
 
-    te: torch.Tensor | None
+    te: torch.Tensor | None = None
     """Echo time [s]."""
 
-    ti: torch.Tensor | None
+    ti: torch.Tensor | None = None
     """Inversion time [s]."""
 
-    fa: torch.Tensor | None
+    fa: torch.Tensor | None = None
     """Flip angle [rad]."""
 
-    tr: torch.Tensor | None
+    tr: torch.Tensor | None = None
     """Repetition time [s]."""
 
-    misc: dict = dataclasses.field(default_factory=dict)
+    _misc: dict = dataclasses.field(default_factory=dict)
     """Dictionary with miscellaneous parameters."""
 
+    position: SpatialDimension[torch.Tensor] = field(
+        default_factory=lambda: SpatialDimension(
+            torch.zeros(1, 1, 1, 1, 1),
+            torch.zeros(1, 1, 1, 1, 1),
+            torch.zeros(1, 1, 1, 1, 1),
+        )
+    )
+    """Center of the excited volume"""
+
+    orientation: Rotation = field(default_factory=lambda: Rotation.identity((1, 1, 1, 1, 1)))
+    """Orientation of the image"""
+
+    patient_table_position: SpatialDimension[torch.Tensor] = field(
+        default_factory=lambda: SpatialDimension(
+            torch.zeros(1, 1, 1, 1, 1),
+            torch.zeros(1, 1, 1, 1, 1),
+            torch.zeros(1, 1, 1, 1, 1),
+        )
+    )
+    """Offset position of the patient table"""
+
+    acquisition_time_stamp: torch.Tensor = field(default_factory=lambda: torch.zeros(1, 1, 1, 1, 1))
+
+    physiology_time_stamps: PhysiologyTimestamps = field(default_factory=PhysiologyTimestamps)
+
+    ImageIdx: ImageIdx = field(default_factory=ImageIdx)
+
     @classmethod
     def from_kheader(cls, kheader: KHeader) -> Self:
         """Create IHeader object from KHeader object.
@@ -74,53 +156,70 @@ def get_item(dataset: Dataset, name: TagType):
             else:
                 raise ValueError(f'Item {name} found {len(found_item)} times.')
 
-        def get_items_from_all_dicoms(name: TagType):
-            """Get list of items for all dataset objects in the list."""
+        def get_items_from_dicom_datasets(name: TagType) -> list:
+            """Get list of items for all datasets in dicom_datasets."""
             return [get_item(ds, name) for ds in dicom_datasets]
 
-        def get_float_items_from_all_dicoms(name: TagType):
-            """Convert items to float."""
-            items = get_items_from_all_dicoms(name)
-            return [float(val) if val is not None else None for val in items]
-
-        def make_unique_tensor(values: Sequence[float]) -> torch.Tensor | None:
-            """If all the values are the same only return one."""
-            if any(val is None for val in values):
+        def get_float_items_from_dicom_datasets(name: TagType) -> list[float]:
+            """Get float items from all dataset in dicom_datasets."""
+            items = []
+            for item in get_items_from_dicom_datasets(name):
+                try:
+                    items.append(float(item))
+                except (TypeError, ValueError):
+                    # None or invalid value
+                    items.append(float('nan'))
+            return items
+
+        def as_5d_tensor(values: Sequence[float]) -> torch.Tensor:
+            """Convert a list of values to a 5d tensor."""
+            tensor = torch.as_tensor(values)
+            tensor = repeat(tensor, 'values-> values 1 1 1 1')
+            tensor = remove_repeat(tensor, 1e-12)
+            return tensor
+
+        def all_nan_to_none(tensor: torch.Tensor) -> torch.Tensor | None:
+            """If all values are nan, return None."""
+            if torch.isnan(tensor).all():
                 return None
-            elif len(np.unique(values)) == 1:
-                return torch.as_tensor([values[0]])
-            else:
-                return torch.as_tensor(values)
-
-        # Conversion functions for units
-        def ms_to_s(ms: torch.Tensor | None) -> torch.Tensor | None:
-            return None if ms is None else ms / 1000
-
-        def deg_to_rad(deg: torch.Tensor | None) -> torch.Tensor | None:
-            return None if deg is None else torch.deg2rad(deg)
-
-        fa = deg_to_rad(make_unique_tensor(get_float_items_from_all_dicoms('FlipAngle')))
-        ti = ms_to_s(make_unique_tensor(get_float_items_from_all_dicoms('InversionTime')))
-        tr = ms_to_s(make_unique_tensor(get_float_items_from_all_dicoms('RepetitionTime')))
-
-        # get echo time(s). Some scanners use 'EchoTime', some use 'EffectiveEchoTime'
-        te_list = get_float_items_from_all_dicoms('EchoTime')
-        if all(val is None for val in te_list):  # check if all entries are None
-            te_list = get_float_items_from_all_dicoms('EffectiveEchoTime')
-        te = ms_to_s(make_unique_tensor(te_list))
-
-        fov_x_mm = get_float_items_from_all_dicoms('Rows')[0] * float(get_items_from_all_dicoms('PixelSpacing')[0][0])
-        fov_y_mm = get_float_items_from_all_dicoms('Columns')[0] * float(
-            get_items_from_all_dicoms('PixelSpacing')[0][1],
-        )
-        fov_z_mm = get_float_items_from_all_dicoms('SliceThickness')[0]
-        fov = SpatialDimension(fov_x_mm, fov_y_mm, fov_z_mm) / 1000  # convert to m
+            return tensor
+
+        fa = all_nan_to_none(deg_to_rad(as_5d_tensor(get_float_items_from_dicom_datasets('FlipAngle'))))
+        ti = all_nan_to_none(ms_to_s(as_5d_tensor(get_float_items_from_dicom_datasets('InversionTime'))))
+        tr = all_nan_to_none(ms_to_s(as_5d_tensor(get_float_items_from_dicom_datasets('RepetitionTime'))))
+
+        te_list = get_float_items_from_dicom_datasets('EchoTime')
+        if all(val is None for val in te_list):
+            # if all 'EchoTime' entries are None, try 'EffectiveEchoTime',
+            # which is used by some scanners
+            te_list = get_float_items_from_dicom_datasets('EffectiveEchoTime')
+        te = all_nan_to_none(ms_to_s(as_5d_tensor(te_list)))
+
+        try:
+            fov_x = mm_to_m(
+                get_float_items_from_dicom_datasets('Rows')[0]
+                * float(get_items_from_dicom_datasets('PixelSpacing')[0][0])
+            )
+        except (TypeError, ValueError):
+            fov_x = float('nan')
+        try:
+            fov_y = mm_to_m(
+                get_float_items_from_dicom_datasets('Columns')[0]
+                * float(get_items_from_dicom_datasets('PixelSpacing')[0][1])
+            )
+        except (TypeError, ValueError):
+            fov_y = float('nan')
+        try:
+            fov_z = mm_to_m(get_float_items_from_dicom_datasets('SliceThickness')[0])
+        except (TypeError, ValueError):
+            fov_z = float('nan')
+        fov = SpatialDimension(fov_z, fov_y, fov_x)
 
         # Get misc parameters
         misc = {}
         for name in MISC_TAGS:
-            misc[name] = make_unique_tensor(get_float_items_from_all_dicoms(MISC_TAGS[name]))
-        return cls(fov=fov, te=te, ti=ti, fa=fa, tr=tr, misc=misc)
+            misc[name] = as_5d_tensor(get_float_items_from_dicom_datasets(MISC_TAGS[name]))
+        return cls(fov=fov, te=te, ti=ti, fa=fa, tr=tr, _misc=misc)
 
     def __repr__(self):
         """Representation method for IHeader class."""