Merge pull request #162 from dvm-shlee/main

[patch] update type annotations for python <3.9 compatibility

brkraw/api/analyzer/affine.py

@@ -3,7 +3,7 @@
 from .base import BaseAnalyzer
 import numpy as np
 from copy import copy
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional
 if TYPE_CHECKING:
     from ..brkobj.scan import ScanInfo
 
@@ -42,7 +42,7 @@ def __init__(self, infoobj: 'ScanInfo'):
         self.subj_type = infoobj.orientation['subject_type'] if hasattr(infoobj, 'orientation') else None
         self.subj_position = infoobj.orientation['subject_position'] if hasattr(infoobj, 'orientation') else None
 
-    def get_affine(self, subj_type:str|None=None, subj_position:str|None=None):
+    def get_affine(self, subj_type: Optional[str] = None, subj_position: Optional[str] = None):
         subj_type = subj_type or self.subj_type
         subj_position = subj_position or self.subj_position
         if isinstance(self.affine, list):
@@ -51,7 +51,7 @@ def get_affine(self, subj_type:str|None=None, subj_position:str|None=None):
             affine = self._correct_orientation(self.affine, subj_position, subj_type)
         return affine
 
-    def _calculate_affine(self, infoobj: 'ScanInfo', slicepack_id:int|None = None):
+    def _calculate_affine(self, infoobj: 'ScanInfo', slicepack_id: Optional[int] = None):
         sidx = infoobj.orientation['orientation_desc'][slicepack_id].index(2) \
             if slicepack_id else infoobj.orientation['orientation_desc'].index(2)
         slice_orient = SLICEORIENT[sidx]

brkraw/api/analyzer/dataarray.py

@@ -2,15 +2,15 @@
 from .base import BaseAnalyzer
 import numpy as np
 from copy import copy
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Union
 if TYPE_CHECKING:
     from ..brkobj import ScanInfo
     from io import BufferedReader
     from zipfile import ZipExtFile
 
 
 class DataArrayAnalyzer(BaseAnalyzer):
-    def __init__(self, infoobj: 'ScanInfo', fileobj: BufferedReader|ZipExtFile):
+    def __init__(self, infoobj: 'ScanInfo', fileobj: Union[BufferedReader, ZipExtFile]):
         infoobj = copy(infoobj)
         self._parse_info(infoobj)
         self.buffer = fileobj

brkraw/api/analyzer/scaninfo.py

@@ -2,7 +2,7 @@
 from collections import OrderedDict
 from brkraw.api import helper
 from .base import BaseAnalyzer
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional, Union
 if TYPE_CHECKING:
     from ..pvobj import PvScan, PvReco, PvFiles
 
@@ -18,8 +18,8 @@ class ScanInfoAnalyzer(BaseAnalyzer):
         NotImplementedError: If an operation is not implemented.
     """
     def __init__(self, 
-                 pvobj: 'PvScan'|'PvReco'|'PvFiles', 
-                 reco_id:int|None = None, 
+                 pvobj: Union['PvScan', 'PvReco', 'PvFiles'], 
+                 reco_id:Optional[int] = None, 
                  debug:bool = False):
 
         self._set_pars(pvobj, reco_id)
@@ -28,7 +28,7 @@ def __init__(self,
             if self.visu_pars:
                 self._parse_info()
 
-    def _set_pars(self, pvobj: 'PvScan'|'PvReco'|'PvFiles', reco_id: int|None):
+    def _set_pars(self, pvobj: Union['PvScan', 'PvReco', 'PvFiles'], reco_id: Optional[int]):
         for p in ['acqp', 'method']:
             try:
                 vals = getattr(pvobj, p)

brkraw/api/brkobj/scan.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+from typing import Optional
 import ctypes
 from ..pvobj import PvScan
 from ..analyzer import ScanInfoAnalyzer, AffineAnalyzer, DataArrayAnalyzer, BaseAnalyzer
@@ -14,8 +15,8 @@ def num_warns(self):
 
 
 class ScanObj(PvScan):
-    def __init__(self, pvscan: 'PvScan', reco_id: int|None = None,
-                 loader_address: int|None = None, debug: bool=False):
+    def __init__(self, pvscan: 'PvScan', reco_id: Optional[int] = None,
+                 loader_address: Optional[int] = None, debug: bool=False):
         super().__init__(pvscan._scan_id, 
                          (pvscan._rootpath, pvscan._path), 
                          pvscan._contents, 
@@ -45,25 +46,25 @@ def get_info(self, reco_id:int, get_analyzer:bool = False):
                     infoobj.warns.extend(attr_vals['warns'])
         return infoobj
 
-    def get_affine_info(self, reco_id:int|None = None):
+    def get_affine_info(self, reco_id:Optional[int] = None):
         if reco_id:
             info = self.get_info(reco_id)
         else:
             info = self.info if hasattr(self, 'info') else self.get_info(self.reco_id)
         return AffineAnalyzer(info)
 
-    def get_data_info(self, reco_id: int|None = None):
+    def get_data_info(self, reco_id: Optional[int] = None):
         reco_id = reco_id or self.avail[0]
         recoobj = self.get_reco(reco_id)
         fileobj = recoobj.get_2dseq()
         info = self.info if hasattr(self, 'info') else self.get_info(self.reco_id)
         return DataArrayAnalyzer(info, fileobj)
 
-    def get_affine(self, reco_id:int|None = None, 
-                   subj_type:str|None = None, subj_position:str|None = None):
+    def get_affine(self, reco_id:Optional[int] = None, 
+                   subj_type:Optional[str] = None, subj_position:Optional[str] = None):
         return self.get_affine_info(reco_id).get_affine(subj_type, subj_position)
 
-    def get_dataarray(self, reco_id: int|None = None):
+    def get_dataarray(self, reco_id: Optional[int] = None):
         return self.get_data_info(reco_id).get_dataarray()
 
     def retrieve_pvscan(self):

brkraw/api/brkobj/study.py

@@ -16,7 +16,7 @@ def get_scan(self, scan_id, reco_id=None, debug=False):
         return ScanObj(pvscan=pvscan, reco_id=reco_id, 
                        loader_address=id(self), debug=debug)
 
-    def _parse_header(self) -> (Dict | None):
+    def _parse_header(self):
         if not self.contents or 'subject' not in self.contents['files']:
             self.header = None
             return

brkraw/api/helper/orientation.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 import math
 import numpy as np
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional
 from .base import BaseHelper, is_all_element_same
 from .slicepack import SlicePack
 if TYPE_CHECKING:
@@ -137,7 +137,7 @@ def _case_multi_slicepacks_multi_slices(self):
         self._orient = orientation
         self._position = positions
 
-    def _est_volume_origin(self, id: int|None =None):
+    def _est_volume_origin(self, id: Optional[int] =None):
         """Estimate the origin coordinates of the Volume matrix.
 
         Notes:

brkraw/app/tonifti/base.py

@@ -7,7 +7,7 @@
 from brkraw.api.brkobj import ScanObj, ScanInfo
 from brkraw.api.analyzer import ScanInfoAnalyzer, DataArrayAnalyzer, AffineAnalyzer
 from .header import Header
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional, Union
 if TYPE_CHECKING:
     from pathlib import Path
 
@@ -25,7 +25,7 @@ class ScaleMode(Enum):
 class BaseMethods:
     info, fileobj = (None, None)
 
-    def set_scale_mode(self, scale_mode:ScaleMode|None):
+    def set_scale_mode(self, scale_mode:Optional[ScaleMode]=None):
         if scale_mode:
             self.scale_mode = scale_mode
         else:
@@ -45,9 +45,9 @@ def _set_info(self):
         self.analysed = analysed
 
     @staticmethod
-    def get_dataobj(scanobj:'ScanInfo'|'ScanObj', 
-                    fileobj:'BufferedReader'|'ZipExtFile'|None = None, 
-                    reco_id:int|None = None,
+    def get_dataobj(scanobj:Union['ScanInfo','ScanObj'], 
+                    fileobj:Union['BufferedReader', 'ZipExtFile', None] = None, 
+                    reco_id:Optional[int] = None,
                     scale_correction:bool = False):
         data_dict = BaseMethods.get_data_dict(scanobj, fileobj, reco_id)
         dataobj = data_dict['data_array']
@@ -62,17 +62,17 @@ def get_dataobj(scanobj:'ScanInfo'|'ScanObj',
         return dataobj
 
     @staticmethod
-    def get_affine(scanobj:'ScanInfo'|'ScanObj', reco_id:int|None = None, 
-                   subj_type:str|None=None, subj_position:str|None=None):
+    def get_affine(scanobj:Union['ScanInfo', 'ScanObj'], reco_id:Optional[int] = None, 
+                   subj_type:Optional[str]=None, subj_position:Optional[str]=None):
         return BaseMethods.get_affine_dict(scanobj, reco_id, subj_type, subj_position)['affine']
 
     @staticmethod
-    def get_data_dict(scanobj:'ScanInfo'|'ScanObj', 
-                      fileobj:'BufferedReader'|'ZipExtFile'|None = None, 
-                      reco_id:int|None = None):
+    def get_data_dict(scanobj:Union['ScanInfo', 'ScanObj'], 
+                      fileobj:Union['BufferedReader', 'ZipExtFile'] = None, 
+                      reco_id:Optional[int] = None):
         if isinstance(scanobj, ScanObj):
             data_info = scanobj.get_data_info(reco_id)
-        elif isinstance(scanobj, ScanInfo) and isinstance(scanobj, BufferedReader|ZipExtFile):
+        elif isinstance(scanobj, ScanInfo) and isinstance(scanobj, Union[BufferedReader, ZipExtFile]):
             data_info = DataArrayAnalyzer(scanobj, fileobj)
         else:
             raise TypeError(
@@ -94,8 +94,8 @@ def get_data_dict(scanobj:'ScanInfo'|'ScanObj',
         }
 
     @staticmethod
-    def get_affine_dict(scanobj:'ScanInfo'|'ScanObj', reco_id:int|None = None,
-                        subj_type:str|None = None, subj_position:str|None = None):
+    def get_affine_dict(scanobj:Union['ScanInfo','ScanObj'], reco_id:Optional[int] = None,
+                        subj_type:Optional[str] = None, subj_position:Optional[str] = None):
         if isinstance(scanobj, ScanObj):
             affine_info = scanobj.get_affine_info(reco_id)
         elif isinstance(scanobj, ScanInfo):
@@ -131,11 +131,11 @@ def get_bdata(analobj:'ScanInfoAnalyzer'):
         return bvals, bvecs
 
     @staticmethod
-    def get_bids_metadata(scaninfo:'ScanInfo', bids_recipe:'Path'|None=None):
+    def get_bids_metadata(scaninfo:'ScanInfo', bids_recipe:Optional['Path']=None):
         print(isinstance(scaninfo, ScanInfo), bids_recipe)
 
     @staticmethod
-    def get_nifti1header(scaninfo:'ScanInfo', scale_mode:'ScaleMode'|None):
+    def get_nifti1header(scaninfo:'ScanInfo', scale_mode:Optional['ScaleMode']=None):
         scale_mode = scale_mode or ScaleMode.HEADER
         return Header(scaninfo, scale_mode).get()
 

brkraw/app/tonifti/brkraw.py

@@ -1,18 +1,18 @@
 from __future__ import annotations
 from brkraw.api.brkobj import StudyObj
 from .base import BaseMethods, ScaleMode
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional
 if TYPE_CHECKING:
     from pathlib import Path
 
 
 class BrkrawToNifti(StudyObj, BaseMethods):
-    def __init__(self, path:'Path', scale_mode: 'ScaleMode'|None = None):
+    def __init__(self, path:'Path', scale_mode: Optional['ScaleMode'] = None):
         """_summary_
 
         Args:
             path (Path): _description_
-            scale_mode (ScaleMode | None, optional): _description_. Defaults to None.
+            scale_mode (ScaleMode , None, optional): _description_. Defaults to None.
         """
 
         super().__init__(path)
@@ -32,40 +32,40 @@ def get_scan(self, scan_id:int):
             self._cache[scan_id] = super().get_scan(scan_id)
         return self._cache[scan_id]
 
-    def get_scan_analyzer(self, scan_id:int, reco_id:int|None=None):
+    def get_scan_analyzer(self, scan_id:int, reco_id:Optional[int]=None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
 
         Returns:
             _type_: _description_
         """
         return self.get_scan(scan_id).get_info(reco_id, get_analyzer=True)
 
-    def get_affine(self, scan_id:int, reco_id:int|None=None, subj_type:str|None=None, subj_position:str|None=None):
+    def get_affine(self, scan_id:int, reco_id:Optional[int]=None, subj_type:Optional[str]=None, subj_position:Optional[str]=None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
-            subj_type (str | None, optional): _description_. Defaults to None.
-            subj_position (str | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
+            subj_type (str , None, optional): _description_. Defaults to None.
+            subj_position (str , None, optional): _description_. Defaults to None.
 
         Returns:
             _type_: _description_
         """
         scanobj = self.get_scan(scan_id)
         return super().get_affine(scanobj=scanobj, reco_id=reco_id, subj_type=subj_type, subj_position=subj_position)
 
-    def get_dataobj(self, scan_id:int, reco_id:int|None=None, scale_mode:'ScaleMode'|None = None):
+    def get_dataobj(self, scan_id:int, reco_id:Optional[int]=None, scale_mode:Optional['ScaleMode'] = None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
-            scale_mode (ScaleMode; | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
+            scale_mode (ScaleMode; , None, optional): _description_. Defaults to None.
 
         Raises:
             ValueError: _description_
@@ -78,27 +78,27 @@ def get_dataobj(self, scan_id:int, reco_id:int|None=None, scale_mode:'ScaleMode'
         scanobj = self.get_scan(scan_id)
         return super().get_dataobj(scanobj=scanobj, fileobj=None, reco_id=reco_id, scale_correction=scale_correction)
 
-    def get_data_dict(self, scan_id:int, reco_id:int|None=None):
+    def get_data_dict(self, scan_id:int, reco_id:Optional[int]=None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
 
         Returns:
             _type_: _description_
         """
         scanobj = self.get_scan(scan_id)
         return super().get_data_dict(scanobj=scanobj, reco_id=reco_id)
 
-    def get_affine_dict(self, scan_id:int, reco_id:int|None=None, subj_type:str|None=None, subj_position:str|None=None):
+    def get_affine_dict(self, scan_id:int, reco_id:Optional[int]=None, subj_type:Optional[str]=None, subj_position:Optional[str]=None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
-            subj_type (str | None, optional): _description_. Defaults to None.
-            subj_position (str | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
+            subj_type (str , None, optional): _description_. Defaults to None.
+            subj_position (str , None, optional): _description_. Defaults to None.
 
         Returns:
             _type_: _description_
@@ -107,13 +107,13 @@ def get_affine_dict(self, scan_id:int, reco_id:int|None=None, subj_type:str|None
         return super().get_affine_dict(scanobj=scanobj, reco_id=reco_id,
                                        subj_type=subj_type, subj_position=subj_position)
 
-    def get_nifti1header(self, scan_id:int, reco_id:int|None=None, scale_mode:'ScaleMode'|None = None):
+    def get_nifti1header(self, scan_id:int, reco_id:Optional[int]=None, scale_mode:Optional['ScaleMode'] = None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
-            scale_mode (ScaleMode | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
+            scale_mode (ScaleMode , None, optional): _description_. Defaults to None.
 
         Returns:
             _type_: _description_
@@ -134,12 +134,12 @@ def get_bdata(self, scan_id:int):
         analobj = self.get_scan_analyzer(scan_id)
         return super().get_bdata(analobj)
 
-    def get_bids_metadata(self, scan_id:int, reco_id:int|None=None, bids_recipe=None):
+    def get_bids_metadata(self, scan_id:int, reco_id:Optional[int]=None, bids_recipe=None):
         """_summary_
 
         Args:
             scan_id (int): _description_
-            reco_id (int | None, optional): _description_. Defaults to None.
+            reco_id (int , None, optional): _description_. Defaults to None.
             bids_recipe (_type_, optional): _description_. Defaults to None.
 
         Returns:

brkraw/app/tonifti/header.py

@@ -1,14 +1,14 @@
 from __future__ import annotations
 import warnings
 from nibabel.nifti1 import Nifti1Header
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Union
 if TYPE_CHECKING:
     from brkraw.api.brkobj import ScanInfo
     from .base import ScaleMode
 
 
 class Header:
-    def __init__(self, scaninfo:'ScanInfo', scale_mode:'ScaleMode'|int):
+    def __init__(self, scaninfo:'ScanInfo', scale_mode:Union['ScaleMode', int]):
         self.info = scaninfo
         self.scale_mode = int(scale_mode)
         self.nifti1header = Nifti1Header()