Merge branch 'development_robert' of github.com:Hendrik-code/TPTBox into development_robert

Author: robert-graf

TPTBox/core/bids_constants.py

@@ -34,7 +34,7 @@
     "MP2RAG",
     "MPM",
     "MT",
-    "MT",
+    "MTS",
     "T1map",
     "T2map",
     "T2starmap",
@@ -164,6 +164,7 @@
     "difference",
     "labels",
     "report",
+    "pet",
 ]
 # https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html
 formats_relaxed = [*formats, "t2", "t1", "t2c", "t1c", "mr", "snapshot", "t1dixon", "dwi", "ctb"]

TPTBox/core/bids_files.py

@@ -687,7 +687,7 @@ def get_changed_bids(
         auto_add_run_id=False,
         additional_folder: str | None = None,
         dataset_path: str | None = None,
-        make_parent=True,
+        make_parent=False,
         non_strict_mode=False,
     ):
         ds = dataset_path if dataset_path is not None else self.get_path_decomposed()[0]
@@ -1108,6 +1108,22 @@ def get_frame_of_reference_uid(self, default=None):
             base36 = chars[i] + base36
         return base36[:length]
 
+    def get_identifier(self, sequence_splitting_keys: list[str]) -> str:
+        """Generates an identifier for the BIDS_FILE based on subject and splitting keys
+
+        Args:
+            sequence_splitting_keys (list[str]): list of keys to use for splitting
+        """
+        if "sub" not in self.info:
+            print(f"family_id, no sub-key, got {self.info}")
+            identifier = "sub-404"
+        else:
+            identifier = "sub-" + self.info["sub"]
+        for s in self.info.keys():
+            if s in sequence_splitting_keys:
+                identifier += "_" + s + "-" + self.info[s]
+        return identifier
+
 
 class Searchquery:
     def __init__(self, subj: Subject_Container, flatten=False) -> None:
@@ -1468,15 +1484,16 @@ def __lt__(self, other):
 
     def get_identifier(self):
         first_e = self.data_dict[next(iter(self.data_dict.keys()))][0]
-        if "sub" not in first_e.info:
-            print(f"family_id, no sub-key, got {first_e.info} and data_dict {list(self.data_dict.keys())}")
-            identifier = "sub-404"
-        else:
-            identifier = "sub-" + first_e.info["sub"]
-        for s in first_e.info.keys():
-            if s in self.sequence_splitting_keys:
-                identifier += "_" + s + "-" + first_e.info[s]
-        return identifier
+        return first_e.get_identifier(self.sequence_splitting_keys)
+        # if "sub" not in first_e.info:
+        #    print(f"family_id, no sub-key, got {first_e.info} and data_dict {list(self.data_dict.keys())}")
+        #    identifier = "sub-404"
+        # else:
+        #    identifier = "sub-" + first_e.info["sub"]
+        # for s in first_e.info.keys():
+        #    if s in self.sequence_splitting_keys:
+        #        identifier += "_" + s + "-" + first_e.info[s]
+        # return identifier
 
     def items(self):
         return self.data_dict.items()

TPTBox/core/dicom/dicom_header_to_keys.py

@@ -279,6 +279,8 @@ def _get(key, default=None):
         found = False
         if modality == "ct":
             mri_format = "ct"
+        elif modality.lower() == "pt":
+            mri_format = "pet"
         elif modality == "xa":  # Angiography
             biplane = False
             if "BIPLANE A" in image_type or "SINGLE A" in image_type:

TPTBox/core/nii_poi_abstract.py

@@ -305,11 +305,12 @@ def assert_affine(
 
         # Print errors
         for err in found_errors:
-            log.print(err, ltype=Log_Type.FAIL, verbose=verbose)
+            text2 = f"{text}; {err}" if text else f"{err}"
+            log.print(f"{text2}", ltype=Log_Type.FAIL, verbose=verbose)
         # Final conclusion and possible raising of AssertionError
         has_errors = len(found_errors) > 0
         if raise_error and has_errors:
-            raise AssertionError(f"{text}; assert_affine failed with {found_errors}")
+            raise AssertionError(f"{text} assert_affine failed with {found_errors}")
 
         return not has_errors
 

TPTBox/core/nii_wrapper.py

@@ -413,6 +413,9 @@ def dtype(self)->type:
         if self.__unpacked:
             return self._arr.dtype # type: ignore
         return self.nii.dataobj.dtype #type: ignore
+    @dtype.setter
+    def dtype(self, dtype:type):
+        self.set_dtype_(dtype)
     @property
     def header(self) -> Nifti1Header:
         if self.__unpacked:
@@ -433,6 +436,9 @@ def affine(self,affine:np.ndarray):
     def orientation(self) -> AX_CODES:
         ort = nio.io_orientation(self.affine)
         return nio.ornt2axcodes(ort) # type: ignore
+    @orientation.setter
+    def orientation(self, value: AX_CODES):
+        self.reorient_(value, verbose=False)
     @property
     def dims(self)->int:
         self._unpack()
@@ -448,6 +454,9 @@ def zoom(self) -> ZOOMS:
             z = z[:n]
         #assert len(z) == 3,z
         return z # type: ignore
+    @zoom.setter
+    def zoom(self, value: tuple[float, float, float]):
+        self.rescale_(value, verbose=False)
 
     @property
     def origin(self) -> tuple[float, float, float]:
@@ -482,10 +491,6 @@ def direction_itk(self) -> list:
         a[:len(a)//3*2]*=-1
         return a.tolist()
 
-    @orientation.setter
-    def orientation(self, value: AX_CODES):
-        self.reorient_(value, verbose=False)
-
 
     def split_4D_image_to_3D(self):
         assert self.get_num_dims() == 4,self.get_num_dims()
@@ -799,9 +804,7 @@ def apply_pad(
         mode: MODES = "constant",
         inplace=False,
         verbose: logging = True
-        ):
-        #TODO add other modes
-        #TODO add testcases and options for modes
+    ):
         if padd is None or padd == 0:
             return self if inplace else self.copy()
 
@@ -824,13 +827,36 @@ def apply_pad(
 
         affine = self.affine @ transform
 
+        arr = self.get_array()
+
+        # ---- 1. CROPPING (negative padding) ----
+        slices = []
+
+        for i, (before, after) in enumerate(padd[:self.dims]):
+            start = max(0, -before)
+            end = arr.shape[i] - max(0, -after)
+            slices.append(slice(start, end))
+
+        # keep non-spatial dims unchanged
+        slices += [slice(None)] * (arr.ndim - self.dims)
+
+        arr = arr[tuple(slices)]
+
+        # ---- 2. PADDING (positive only) ----
+        padd_positive = tuple(
+            (max(0, b), max(0, a)) for b, a in padd
+        )
+
         args = {}
         if mode == "constant":
             args["constant_values"] = self.get_c_val()
 
+        if mode == "nearest":
+            mode = "edge"
+
         log.print(f"Padd {padd}; {mode=}, {args}", verbose=verbose)
 
-        arr = np.pad(self.get_array(), padd, mode=mode, **args)
+        arr = np.pad(arr, padd_positive, mode=mode, **args)
 
         nii = (arr, affine, self.header)
 
@@ -935,35 +961,38 @@ def resample_from_to(self, to_vox_map:Image_Reference|Has_Grid|tuple[SHAPE,AFFIN
             mapping = to_vox_map.to_gird()
         else:
             mapping = to_vox_map if isinstance(to_vox_map, tuple) else to_nii_optional(to_vox_map, seg=self.seg, default=to_vox_map)
-        if isinstance(mapping,Has_Grid) and mapping.assert_affine(self,raise_error=False,origin_tolerance=0.000001,error_tolerance=0.000001,shape_tolerance=0):
-            log.print(f"resample_from_to skipped; already in space: {self}",verbose=verbose)
-            return self if inplace else self.copy()
-
-            #m1 = mapping.make_empty_POI().reorient(self.orientation)
-            #if m1.assert_affine(self,raise_error=False,origin_tolerance=0.000001,error_tolerance=0.000001,shape_tolerance=0):
-            #    log.print(f"resample_from_to only need reorientation; {self.orientation}",verbose=verbose)
-            #    return self.reorient(mapping.orientation,inplace=inplace)
-            #if self.orientation == mapping.orientation and self.zoom == mapping.zoom:
-            #    shift = (np.array(self.origin) - np.array(m1.origin)) / np.array(m1.zoom)
-            #    if np.allclose(shift, np.round(shift), atol=1e-6):
-            #        self = self.reorient(mapping.orientation,inplace=inplace)  # noqa: PLW0642
-            #        shift = (np.array(self.origin) - np.array(mapping.origin)) / np.array(mapping.zoom)
-            #        shift = np.round(shift).astype(int)
-            #        src_shape = np.array(mapping.shape)
-            #        dst_shape = np.array(self.shape)
-            #        # padding before = how much dst starts before src
-            #        pad_before = np.maximum(-shift, 0)
-            #
-            #        # where src ends inside dst
-            #        src_end_in_dst = shift + src_shape
-            #        # padding after = remaining dst size after src
-            #        pad_after = np.maximum(dst_shape - src_end_in_dst, 0)
-            #        pad = tuple((int(b), int(a)) for b, a in zip(pad_before, pad_after))
-            #        ret = self.apply_pad(pad, mode=mode)
-            #
-            #        log.print(f"resample_from_to only needs padding/cropping {pad}, ",verbose=verbose,)
-            #        ret.assert_affine(mapping,raise_error=False,origin_tolerance=0.000001,error_tolerance=0.000001,shape_tolerance=0)
-            #        return ret
+        if isinstance(mapping,Has_Grid):
+            if mapping.assert_affine(self,raise_error=False,origin_tolerance=0.000001,error_tolerance=0.000001,shape_tolerance=0):
+                log.print(f"resample_from_to skipped; already in space: {self}",verbose=verbose)
+                return self if inplace else self.copy()
+
+            m1 = mapping if mapping.orientation == self.orientation else mapping.make_empty_POI().reorient(self.orientation)
+            if m1.assert_affine(self,raise_error=False,origin_tolerance=0.00001,error_tolerance=0.00001,shape_tolerance=0):
+                log.print(f"resample_from_to only need reorientation; {self.orientation}",verbose=verbose)
+                ret = self.reorient(mapping.orientation,inplace=inplace)
+                ret.affine = mapping.affine #remove floating point error
+                return ret
+            if self.orientation == mapping.orientation and np.allclose(self.zoom , mapping.zoom, atol=1e-6):
+                shift = (np.array(self.origin) - np.array(m1.origin)) / np.array(m1.zoom)
+                if np.allclose(shift, np.round(shift), atol=1e-6):
+                    s = self.reorient(mapping.orientation,inplace=inplace)  # noqa: PLW0642
+                    shift = (np.array(self.origin) - np.array(mapping.origin)) / np.array(mapping.zoom)
+                    shift = np.round(shift).astype(int)
+                    dst_shape = np.array(mapping.shape)
+                    src_shape = np.array(s.shape)
+                    # padding before = how much dst starts before src
+                    pad_before = shift
+                    # padding after = remaining dst size after src
+                    pad_after = dst_shape-shift-src_shape
+                    pad = tuple((int(b), int(a)) for b, a in zip(pad_before, pad_after))
+                    ret = s.apply_pad(pad, mode=mode,inplace=inplace,verbose=verbose)
+
+                    #TODO SET raise_error=False before committing
+                    valid = ret.assert_affine(mapping,raise_error=True,origin_tolerance=0.0001,error_tolerance=0.0001,shape_tolerance=0)
+                    if valid:
+                        log.print(f"resample_from_to only needs padding/cropping {pad}",verbose=verbose)
+                        ret.affine = mapping.affine #remove floating point error
+                        return ret
 
 
         assert mapping is not None
@@ -1772,7 +1801,7 @@ def infect(self: NII, reference_mask: NII, inplace=False,verbose=True,axis:int|s
         """
         self.assert_affine(reference_mask)
         if _do_crop:
-            crop = reference_mask.compute_crop(0,5)
+            crop = reference_mask.compute_crop(0,5,raise_error=False)
             s = self.apply_crop(crop)
             reference_mask = reference_mask.apply_crop(crop)
         else:

TPTBox/core/np_utils.py

@@ -563,7 +563,7 @@ def np_calc_crop_around_centerpoint(
     arr: np.ndarray,
     cutout_size: tuple[int, ...],
     pad_to_size: Sequence[int] | np.ndarray | int = 0,
-) -> tuple[np.ndarray, tuple, tuple]:
+) -> tuple[np.ndarray, tuple[slice, slice, slice], tuple]:
     """
 
     Args:
@@ -944,7 +944,7 @@ def np_get_connected_components_center_of_mass(
         connectivity=connectivity,
         label_ref=label,
     )
-    coms = list(np_center_of_mass(subreg_cc[label]).values())
+    coms = list(np_center_of_mass(subreg_cc[label]).values()) if label in subreg_cc else None
 
     if sort_by_axis is not None:
         coms.sort(key=lambda a: a[sort_by_axis])
@@ -1050,7 +1050,7 @@ def np_fill_holes(
         else:
             assert 0 <= slice_wise_dim <= arr.ndim - 1, f"slice_wise_dim needs to be in range [0, {arr.ndim - 1}]"
             filled = np.swapaxes(arr_lc.copy(), 0, slice_wise_dim)
-            filled = np.stack([_fill(x) for x in filled])
+            filled = np.stack([_fill(x).astype(arr.dtype) for x in filled])
             filled = np.swapaxes(filled, 0, slice_wise_dim)
         filled[filled != 0] = l
         if use_crop:

TPTBox/core/poi.py

@@ -945,10 +945,10 @@ def calc_poi_from_subreg_vert(
     save_buffer_file=False,  # used by wrapper  # noqa: ARG001
     decimals=2,
     subreg_id: int | Abstract_lvl | Sequence[int | Abstract_lvl] | Sequence[Abstract_lvl] | Sequence[int] = 50,
-    verbose: logging = True,
+    verbose: logging = False,
     extend_to: POI | None = None,
     # use_vertebra_special_action=True,
-    _vert_ids=None,
+    _vert_ids: list[int] | None = None,
     _print_phases=False,
     _orientation_version=0,
 ) -> POI:
@@ -1088,6 +1088,7 @@ def calc_poi_from_subreg_vert(
             subreg_msk,
             _vert_ids=_vert_ids,
             log=log,
+            verbose=verbose,
             _orientation_version=_orientation_version,
         )
     extend_to.apply_crop_reverse(crop, org_shape, inplace=True)

TPTBox/core/poi_fun/poi_abstract.py

@@ -441,7 +441,7 @@ def map_labels_(
 
     def sort(self, inplace=True, order_dict: dict | None = None) -> Self:
         """Sort vertebra dictionary by sorting_list"""
-        if self.level_one_info is not None:
+        if self.level_one_info is not None and self.level_one_info != Any:
             order_dict = self.level_one_info.order_dict()
         poi = self.centroids._sort(inplace=inplace, order_dict=order_dict)
         if inplace: