Merge pull request #100 from Hendrik-code/development_robert

Development robert

Author: Hendrik-code

TPTBox/core/bids_constants.py

@@ -4,6 +4,7 @@
 
 formats = [
     "ct",
+    "cta",
     "dixon",
     "T2c",
     "T1c",
@@ -163,7 +164,7 @@
     "labels",
 ]
 # https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html
-formats_relaxed = [*formats, "t2", "t1", "t2c", "t1c", "cta", "mr", "snapshot", "t1dixon", "dwi"]
+formats_relaxed = [*formats, "t2", "t1", "t2c", "t1c", "mr", "snapshot", "t1dixon", "dwi", "ctb"]
 # Recommended writing style: T1c, T2c; This list is not official and can be extended.
 
 modalities = {

TPTBox/core/bids_files.py

@@ -664,7 +664,10 @@ def bids_format(self):
 
     @property
     def mod(self):
-        return self.mod
+        mod = self.bids_format
+        if mod == "msk":
+            return self.get("mod")
+        return mod
 
     def get_parent(self, file_type=None):
         return self.get_path_decomposed(file_type)[1]
@@ -985,7 +988,8 @@ def open_nii(self):
         except KeyError as e:
             raise ValueError(f"nii.gz not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e
 
-    def get_grid_info(self):
+    def get_grid_info(self, add_grid_info_to_json=True):
+        """returns the Grid info. It looks up if this info is in json. If not it loads the File, computes the Grid and saves it in the json"""
         from TPTBox.core.dicom.dicom_extract import _add_grid_info_to_json
         from TPTBox.core.nii_poi_abstract import Grid
 
@@ -994,7 +998,7 @@ def get_grid_info(self):
             return None
         if not self.has_json():
             self.file["json"] = Path(str(nii_file).split(".")[0] + ".json")
-        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"])["grid"])
+        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"], add=add_grid_info_to_json)["grid"])
 
     def get_nii_file(self) -> Path:  # type: ignore
         for key in _supported_nii_files:

TPTBox/core/dicom/dicom2nii_utils.py

@@ -243,7 +243,7 @@ def test_name_conflict(json_ob, file):
     return False
 
 
-def save_json(json_ob, file, check_exist=False):
+def save_json(json_ob, file, check_exist=False, override=True):
     """
     recieves a json object and a path and saves the object as a json file
     """
@@ -257,8 +257,9 @@ def convert(obj):
 
     if check_exist and test_name_conflict(json_ob, file):
         raise FileExistsError(file)
-    if Path(file).exists():
+    if Path(file).exists() and not override:
         return True
+    Print_Logger().on_save("save json with grid info", file)
     with open(file, "w") as file_handel:
         json.dump(json_ob, file_handel, indent=4, default=convert)
     return False

TPTBox/core/dicom/dicom_extract.py

@@ -316,11 +316,12 @@ def _from_dicom_to_nii(
     return nii_path if suc else None
 
 
-def _add_grid_info_to_json(nii_path: Path | str, simp_json: Path | str, force_update=False):
-    nii = NII.load(nii_path, False)
+def _add_grid_info_to_json(nii_path: Path | str, simp_json: Path | str, force_update=False, add=True):
     json_dict = load_json(simp_json) if Path(simp_json).exists() else {}
     if "grid" in json_dict and not force_update:
         return json_dict
+    print("Read Grid info", Path(simp_json).exists(), "grid" in json_dict)
+    nii = NII.load(nii_path, False)
     gird = {
         "shape": nii.shape,
         "spacing": nii.spacing,
@@ -330,7 +331,7 @@ def _add_grid_info_to_json(nii_path: Path | str, simp_json: Path | str, force_up
         "dims": nii.get_num_dims(),
     }
     json_dict["grid"] = gird
-    save_json(json_dict, simp_json)
+    save_json(json_dict, simp_json, override=add)
     return json_dict
 
 

TPTBox/core/dicom/dicom_header_to_keys.py

@@ -222,7 +222,7 @@ def _get(key, default=None):
             keys["acq"] = to_nii(dcm_data_l).get_plane(1)
         else:
             keys["acq"] = get_plane_dicom(dcm_data_l, 1)
-        keys["part"] = dixon_mapping.get(_get("ProtocolName", "NO-PART").split("_")[-1], None)
+        keys["part"] = dixon_mapping.get(_get("ProtocolName", "NO-PART").split("_")[-1])
 
         sequ = _get("SeriesNumber", None)
         if sequ is None:

TPTBox/core/internal/ants_load.py

@@ -2,7 +2,6 @@
 
 from typing import TYPE_CHECKING
 
-import ants
 import numpy as np
 
 if TYPE_CHECKING:
@@ -23,6 +22,8 @@ def nifti_to_ants(nib_image: Nifti1Image, **args):
     ants_image : ants.ANTsImage
         The converted ANTs image.
     """
+    import ants
+
     try:
         return ants.utils.from_nibabel_nifti(nib_image, **args)
     except Exception:
@@ -111,6 +112,8 @@ def ants_to_nifti(img, header=None) -> Nifti1Image:
     img : Nifti1Image
         The converted Nifti image.
     """
+    import ants
+
     try:
         return ants.utils.to_nibabel_nifti(img, header=header)
     except Exception:
@@ -131,6 +134,7 @@ def ants_to_nifti(img, header=None) -> Nifti1Image:
 to_nibabel = ants_to_nifti
 
 if __name__ == "__main__":
+    import ants
     import nibabel as nib
 
     fn = ants.get_ants_data("mni")

TPTBox/core/internal/slicer_nrrd.py

@@ -399,9 +399,38 @@ def _write_segmentation(file, segmentation, compression_level=9, index_order=Non
 
     # Get list of segment IDs (needed if we need to generate new ID)
     segment_ids = set()
-    for _, segment in enumerate(segmentation["segments"]):
+    segment_ids_num = set()
+    for _, segment in enumerate(segmentation.get("segments", [])):
         if "id" in segment:
             segment_ids.add(segment["id"])
+            segment_ids_num.add(segment["labelValue"])
+    from TPTBox.core.np_utils import np_unique_withoutzero
+    from TPTBox.mesh3D.mesh_colors import get_color_by_label
+
+    if "segments" not in segmentation:
+        segmentation["segments"] = []
+    for i in np_unique_withoutzero(voxels):
+        if i in segment_ids_num:
+            continue
+        l: list = segmentation["segments"]
+        segment_ids.add(f"Segment_{i}")
+        l.append(
+            {
+                "id": f"Segment_{i}",
+                "color": get_color_by_label(i).rgb / 255.0,
+                "colorAutoGenerated": False,
+                "labelValue": i,
+                "layer": 0,
+                "name": f"Segment_{i}",
+                "nameAutoGenerated": True,
+                "terminology": {
+                    "contextName": "TPTBox colors",
+                    "category": ["SCT", "85756007", "Tissue"],
+                    "type": ["SCT", "85756007", "Tissue"],
+                    "anatomicContextName": "Undefined",
+                },
+            }
+        )
 
     for output_segment_index, segment in enumerate(segmentation["segments"]):
         # Copy all segment fields corresponding to this segment
@@ -694,7 +723,7 @@ def save_slicer_nrrd(nii: NII, file: str | Path, make_parents=True, verbose: log
         **info,
     }
     if nii.seg:
-        segmentation["containedRepresentationNames"] = info.get("containedRepresentationNames", ["Binary labelmap"])
+        segmentation["containedRepresentationNames"] = info.get("containedRepresentationNames", ["Binary labelmap", "Closed surface"])
         segmentation["masterRepresentation"] = info.get("masterRepresentation", "Binary labelmap")
         segmentation["referenceImageExtentOffset"] = info.get("referenceImageExtentOffset", [0, 0, 0])
     remove_not_supported_values(segmentation)

TPTBox/core/nii_poi_abstract.py

@@ -57,7 +57,8 @@ def to_gird(self) -> Grid:
 
     @property
     def shape_int(self):
-        assert self.shape is not None, "need shape information"
+        if self.shape is None:
+            return None
         return tuple(np.rint(list(self.shape)).astype(int).tolist())
 
     @property

TPTBox/core/nii_wrapper.py

@@ -58,7 +58,6 @@
     MODES,
     SHAPE,
     ZOOMS,
-    Location,
     _same_direction,
     log,
     logging,
@@ -309,13 +308,22 @@ def _unpack(self):
         try:
             if self.__unpacked:
                 return
-            if not self._checked_dtype or self.seg:
-                dtype = _check_if_nifty_is_lying_about_its_dtype(self)
-                #print("unpack-nii",f"{self.seg=}",dtype)
-                self._checked_dtype = True
-                self._arr = np.asanyarray(self.nii.dataobj, dtype=dtype).copy()
-            else:
-                self._arr = np.asanyarray(self.nii.dataobj, dtype=self.nii.dataobj.dtype).copy() #type: ignore
+            try:
+                #if arr.dtype.fields is not None:  # structured dtype (RGB)
+                #    arr = np.stack([arr[name] for name in arr.dtype.names], axis=-1)
+                if not self._checked_dtype or self.seg:
+                    dtype = _check_if_nifty_is_lying_about_its_dtype(self)
+                    #print("unpack-nii",f"{self.seg=}",dtype)
+                    self._checked_dtype = True
+                    self._arr = np.asanyarray(self.nii.dataobj, dtype=dtype).copy()
+                else:
+                    self._arr = np.asanyarray(self.nii.dataobj, dtype=self.nii.dataobj.dtype).copy() #type: ignore
+            except np.exceptions.DTypePromotionError:
+                arr = np.asarray(self.nii.dataobj)
+                if arr.dtype.fields is not None:  # structured dtype (RGB)
+                    self._arr = np.stack([arr[name] for name in arr.dtype.names], axis=-1)
+                else:
+                    raise np.exceptions.DTypePromotionError(f"The DTypes <class '{self.nii.dataobj.dtype}'> do not have a common numerical DType. {np.asarray(self.nii.dataobj)}") from None
 
             self._aff = self.nii.affine
             self._header:Nifti1Header = self.nii.header # type: ignore
@@ -779,9 +787,11 @@ def pad_to(self,target_shape:list[int]|tuple[int,int,int] | Self, mode:MODES="co
             s = s.apply_crop(tuple(crop),inplace=inplace)
         return s.apply_pad(padding,inplace=inplace,mode=mode)
 
-    def apply_pad(self,padd:Sequence[tuple[int|None,int]],mode:MODES="constant",inplace = False,verbose:logging=True):
+    def apply_pad(self,padd:Sequence[tuple[int|None,int]]|None,mode:MODES="constant",inplace = False,verbose:logging=True):
         #TODO add other modes
         #TODO add testcases and options for modes
+        if padd is None:
+            return self if inplace else self.copy()
         transform = np.eye(self.dims+1, dtype=int)
         assert len(padd) == self.dims
         for i, (before,_) in enumerate(padd):
@@ -1518,7 +1528,9 @@ def is_segmentation_in_border(self,minimum=0, voxel_tolerance: int = 2,use_mm=Fa
         Returns:
         - bool: True if the segmentation is within the defined voxel tolerance of the border, False otherwise.
         """
-        slices = self.compute_crop(minimum,dist=0,use_mm=use_mm)
+        slices = self.compute_crop(minimum,dist=0,use_mm=use_mm,raise_error=False)
+        if slices is None:
+            return False
         shp = self.shape
         seg_at_border = False
         for d in range(3):
@@ -1567,7 +1579,7 @@ def truncate_labels_beyond_reference_(
         if len(threshold[axis_]) == 0:
             return self if inplace else self.copy()
         flip_up = flip
-        if inclusion:
+        if not inclusion:
             flip_up = not flip_up
         # Determine the lowest index along the axis
         limit = threshold[axis_].min() if flip_up else threshold[axis_].max()
@@ -1593,11 +1605,12 @@ def truncate_labels_beyond_reference(
         not_beyond: int | list[int] = 1,
         fill: int = 0,
         axis: DIRECTIONS = "S",
-        inclusion: bool = False
+        inclusion: bool = False,
+        inplace=False
     ):
-        return self.truncate_labels_beyond_reference_(idx,not_beyond,fill,axis,inclusion)
+        return self.truncate_labels_beyond_reference_(idx,not_beyond,fill,axis,inclusion,inplace=inplace)
 
-    def infect(self: NII, reference_mask: NII, inplace=False,verbose=True,axis:int|str|None=None):
+    def infect(self: NII, reference_mask: NII, inplace=False,verbose=True,axis:int|str|None=None,max_depth=None):
         """
         Expands labels from self_mask into regions of reference_mask == 1 via breadth-first diffusion.
 
@@ -1633,7 +1646,7 @@ def infect(self: NII, reference_mask: NII, inplace=False,verbose=True,axis:int|s
 
         search = []
         coords = np.where(self_mask != 0)
-        def _add_idx(x,y,z,v):
+        def _add_idx(x,y,z,v,d):
             for x1,y1,z1 in kernel:
                 a = x+x1
                 b = y+y1
@@ -1644,27 +1657,29 @@ def _add_idx(x,y,z,v):
                     continue
                 #try:
                 if searched[a,b,c] == 0 and ref_mask[a,b,c] == 1:
-                    search.append((a,b,c,v))
+                    search.append((a,b,c,v,d))
                 #except Exception:
                 #    pass
-        def _infect(a,b,c,v):
+        def _infect(a,b,c,v,d):
+            if d-1 == max_depth:
+                return
             if searched[a,b,c] != 0:
                 return
             if ref_mask[a,b,c] == 0:
                 return
             #print(a,b,c)
             searched[a,b,c] = 1
             self_mask[a,b,c] = v
-            _add_idx(x,y,z,v)
+            _add_idx(x,y,z,v,d)
 
         from tqdm import tqdm
         for x,y,z in tqdm(zip(coords[0],coords[1],coords[2]),total=len(coords[0]),disable=not verbose,desc="Collecting Surface"):
-            _add_idx(x,y,z,self_mask[x,y,z])
+            _add_idx(x,y,z,self_mask[x,y,z],0)
         while len(search) != 0:
             search2 = search
             search = []
-            for x,y,z,v in tqdm(search2,disable=not verbose,desc="infect"):
-                _infect(x,y,z,v)
+            for x,y,z,v,d in tqdm(search2,disable=not verbose,desc="infect"):
+                _infect(x,y,z,v,d+1)
         self_mask[self_mask == 0] = self_mask_org[self_mask == 0]
         return self.set_array(self_mask,inplace=inplace)
 
@@ -1897,9 +1912,9 @@ def extract_label(self,label:int|Enum|Sequence[int]|Sequence[Enum]|None, keep_la
         if keep_label:
             seg_arr = seg_arr * self.get_seg_array()
         return self.set_array(seg_arr,inplace=inplace)
-    def extract_label_(self,label:int|Location|Sequence[int]|Sequence[Location], keep_label=False):
+    def extract_label_(self,label:int|Enum|Sequence[int]|Sequence[Enum], keep_label=False):
         return self.extract_label(label,keep_label,inplace=True)
-    def remove_labels(self,label:int|Location|Sequence[int]|Sequence[Location], inplace=False, verbose:logging=True, removed_to_label=0):
+    def remove_labels(self,label:int|Enum|Sequence[int]|Sequence[Enum], inplace=False, verbose:logging=True, removed_to_label=0):
         '''If this NII is a segmentation you can single out one label.'''
         assert label != 0, 'Zero label does not make sens.  This is the background'
         seg_arr = self.get_seg_array()
@@ -1912,18 +1927,25 @@ def remove_labels(self,label:int|Location|Sequence[int]|Sequence[Location], inpl
             else:
                 seg_arr[seg_arr == l] = removed_to_label
         return self.set_array(seg_arr,inplace=inplace, verbose=verbose)
-    def remove_labels_(self,label:int|Location|Sequence[int]|Sequence[Location], verbose:logging=True):
-        return self.remove_labels(label,inplace=True,verbose=verbose)
+    def remove_labels_(self,label:int|Enum|Sequence[int]|Sequence[Enum],removed_to_label=0, verbose:logging=True):
+        return self.remove_labels(label,inplace=True,removed_to_label=removed_to_label,verbose=verbose)
     def apply_mask(self,mask:Self, inplace=False):
         assert mask.shape == self.shape, f"[def apply_mask] Mask and Shape are not equal: \nMask - {mask},\nSelf - {self})"
         seg_arr = mask.get_seg_array()
         seg_arr[seg_arr != 0] = 1
         arr = self.get_array()
         return self.set_array(arr*seg_arr,inplace=inplace)
 
-    def unique(self,verbose:logging=False):
+    def unique(self,verbose:logging=False,crop=False):
         '''Returns all integer labels WITHOUT 0. Must be performed only on a segmentation nii'''
-        out = np_unique_withoutzero(self.get_seg_array())
+
+        arr = self.get_seg_array()
+        if crop:
+            try:
+                arr = arr[np_bbox_binary(arr)]
+            except Exception:
+                pass
+        out = np_unique_withoutzero(arr)
         log.print(out,verbose=verbose)
         return out
     def voxel_volume(self):

TPTBox/core/nii_wrapper_math.py

@@ -184,11 +184,15 @@ def mean(self,axis = None,keepdims=False,where = np._NoValue, **qargs)->float:
             where=where.get_array().astype(bool)
 
         return np.mean(self.get_array(),axis=axis,keepdims=keepdims,where=where,**qargs)
-    def median(self,axis = None,keepdims=False,where = np._NoValue, **qargs)->float:  # type: ignore
+    def median(self, axis=None, keepdims=False,  **qargs):  # type: ignore
+        arr = self.get_array()
+        return np.median(arr, axis=axis, keepdims=keepdims, **qargs)
+
+    def std(self,axis = None,keepdims=False,where = np._NoValue, **qargs)->float:  # type: ignore
         if hasattr(where,"get_array"):
             where=where.get_array().astype(bool)
 
-        return np.median(self.get_array(),axis=axis,keepdims=keepdims,where=where,**qargs)
+        return np.std(self.get_array(),axis=axis,keepdims=keepdims,where=where,**qargs)
     def threshold(self,threshold=0.5, inplace=False):
         arr = self.get_array()
         arr2 = arr.copy()