Changes

arg_types.py - update unquote_str docstring common.py - remove the obsolete removesuffix function run_prediction.py - remove the obsolete removesuffix function quick_qc.py - Fix the docstring of get_region_by_intersection_mask generate_hdf5.py - replace seg-mask with sag_mask interpolation_layer.py - Update of the crop_position property common.py - Update the docstrings of pipeline and iterate
Deep-MI · Feb 8, 2024 · bb0ea35 · bb0ea35
1 parent e1f72e4
commit bb0ea35
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diff --git a/FastSurferCNN/generate_hdf5.py b/FastSurferCNN/generate_hdf5.py
@@ -155,7 +155,7 @@ def __init__(self, params: Dict, processing: str = "aparc"):
         self.gm_mask = params["gm_mask"]
 
         self.lut = read_classes_from_lut(params["lut"])
-        self.labels, self.labels_sag = get_labels_from_lut(self.lut, params["sag-mask"])
+        self.labels, self.labels_sag = get_labels_from_lut(self.lut, params["sag_mask"])
         self.lateralization = unify_lateralized_labels(self.lut, params["combi"])
 
         if params["csv_file"] is not None:
@@ -540,7 +540,7 @@ def create_hdf5_dataset(self, blt: int):
         "plane": args.plane,
         "lut": args.lut,
         "combi": args.combi,
-        "sag-mask": args.sag_mask,
+        "sag_mask": args.sag_mask,
         "hires_weight": args.hires_w,
         "gm_mask": args.gm,
         "gradient": not args.no_grad,

diff --git a/FastSurferCNN/models/interpolation_layer.py b/FastSurferCNN/models/interpolation_layer.py
@@ -36,23 +36,23 @@ class _ZoomNd(nn.Module):
     Attributes
     ----------
     _mode
-        Interpolation mode as in `torch.nn.interpolate` (default: 'neareast').
+        (Protected) Interpolation mode as in `torch.nn.interpolate` (default: 'neareast').
     _target_shape
-        Target tensor size for after this module,
+        (Protected) Target tensor size for after this module,
         not including batchsize and channels.
     _N
-        Number of dimensions.
+        (Protected) Internal number of dimensions.
 
     Methods
     -------
     forward
         Forward propagation.
     _fix_scale_factors
-        Checking and fixing the conformity of scale_factors.
+        (Protected) Checking and fixing the conformity of scale_factors.
     _interpolate
-        Abstract method.
-    -calculate_crop_pad
-        Return start- and end- coordinate.
+        (Protected) Abstract method.
+    _calculate_crop_pad
+        (Protected) Return start- and end- coordinate.
     """
 
     def __init__(
@@ -376,6 +376,8 @@ class Zoom2d(_ZoomNd):
         (Protected) Crops, interpolates and pads the tensor.
     """
 
+    _crop_position: str
+
     def __init__(
         self,
         target_shape: _T.Optional[_T.Sequence[int]],
@@ -398,6 +400,28 @@ def __init__(
         if interpolation_mode not in ["nearest", "bilinear", "bicubic", "area"]:
             raise ValueError(f"invalid interpolation_mode, got {interpolation_mode}")
 
+        self._N = 2
+        super(Zoom2d, self).__init__(target_shape, interpolation_mode)
+        self.crop_position = crop_position
+
+    @property
+    def crop_position(self) -> str:
+        """
+        Property associated with the position of the image in the data.
+        """
+        return self._crop_position
+
+    @crop_position.setter
+    def crop_position(self, crop_position: str) -> None:
+        """
+        Set the crop position.
+
+        Parameters
+        ----------
+        crop_position : str
+            The crop position key from 'top_left', 'bottom_left', top_right', 
+            'bottom_right', 'center'.
+        """
         if crop_position not in [
             "top_left",
             "bottom_left",
@@ -406,11 +430,8 @@ def __init__(
             "center",
         ]:
             raise ValueError(f"invalid crop_position, got {crop_position}")
-
-        self._N = 2
-        super(Zoom2d, self).__init__(target_shape, interpolation_mode)
-        self.crop_position = crop_position
-
+        self._crop_position = crop_position        
+
     def _interpolate(
         self,
         data: Tensor,
@@ -514,6 +535,29 @@ def __init__(
         if interpolation_mode not in ["nearest", "trilinear", "area"]:
             raise ValueError(f"invalid interpolation_mode, got {interpolation_mode}")
 
+        self._N = 3
+        super(Zoom3d, self).__init__(target_shape, interpolation_mode)
+        self.crop_position = crop_position
+
+    @property
+    def crop_position(self) -> str:
+        """
+        Property associated with the position of the image in the data.
+        """
+        return self._crop_position
+
+    @crop_position.setter
+    def crop_position(self, crop_position: str) -> None:
+        """
+        Set the crop position.
+
+        Parameters
+        ----------
+        crop_position : str
+            Crop position to use from 'front_top_left', 'back_top_left',
+            'front_bottom_left', 'back_bottom_left', 'front_top_right', 'back_top_right',
+            'front_bottom_right', 'back_bottom_right', 'center' (default: 'front_top_left').
+        """
         if crop_position not in [
             "front_top_left",
             "back_top_left",
@@ -526,11 +570,8 @@ def __init__(
             "center",
         ]:
             raise ValueError(f"invalid crop_position, got {crop_position}")
-
-        self._N = 3
-        super(Zoom3d, self).__init__(target_shape, interpolation_mode)
         self._crop_position = crop_position
-
+    
     def _interpolate(
         self, data: Tensor, scale_factor: _T.Union[Tensor, np.ndarray, _T.Sequence[int]]
     ):

diff --git a/FastSurferCNN/quick_qc.py b/FastSurferCNN/quick_qc.py
@@ -100,7 +100,7 @@ def check_volume(asegdkt_segfile:np.ndarray, voxvol: float, thres: float = 0.70)
 def get_region_bg_intersection_mask(
     seg_array, region_labels=VENT_LABELS, bg_label=BG_LABEL
 ):
-    """
+    f"""
     Return a mask of the intersection between the voxels of a given region and background voxels.
 
     This is obtained by dilating the region by 1 voxel and computing the intersection with the
@@ -112,18 +112,22 @@ def get_region_bg_intersection_mask(
     ----------
     seg_array : numpy.ndarray
         Segmentation array.
-    region_labels : Dict
-        Dictionary whose values correspond to the desired region's labels (Default value = VENT_LABELS).
-        VENT_LABELS is a dictionary containing labels for different regions related to the ventricles,
-        such as "Left-Lateral-Ventricle", "Right-Lateral-Ventricle", etc., along with their 
-        corresponding numeric values.
-    bg_label : int,  default="BG_LABEL"
-        (Default value = BG_LABEL).
+    region_labels : dict, default=<dict VENT_LABELS>
+        Dictionary whose values correspond to the desired region's labels (see Note).
+    bg_label : int,  default={BG_LABEL}
+        (Default value = {BG_LABEL}).
 
     Returns
     -------
     bg_intersect : numpy.ndarray
         Region and background intersection mask array.
+
+    Notes
+    -----
+    VENT_LABELS is a dictionary containing labels for four regions related to the ventricles:
+    "Left-Lateral-Ventricle", "Right-Lateral-Ventricle", "Left-choroid-plexus", 
+    "Right-choroid-plexus" along with their corresponding integer label values 
+    (see also FreeSurferColorLUT.txt).
     """
     region_array = seg_array.copy()
     conditions = np.all(

diff --git a/FastSurferCNN/run_prediction.py b/FastSurferCNN/run_prediction.py
@@ -107,37 +107,6 @@ def args2cfg(
     return cfg_fin, cfg_cor, cfg_sag, cfg_ax
 
 
-def removesuffix(string: str, suffix: str) -> str:
-    """
-    Remove a suffix from a string.
-
-    Similar to string.removesuffix in PY3.9+,
-
-    Parameters
-    ----------
-    string : str
-        String to be cut.
-    suffix : str
-        Suffix to be removed.
-
-    Returns
-    -------
-    Str
-        Suffix removed string.
-    """
-    import sys
-
-    if sys.version_info.minor >= 9:
-        # removesuffix is a Python3.9 feature
-        return string.removesuffix(suffix)
-    else:
-        return (
-            string[: -len(suffix)]
-            if len(suffix) > 0 and string.endswith(suffix)
-            else string
-        )
-
-
 ##
 # Input array preparation
 ##

diff --git a/FastSurferCNN/utils/arg_types.py b/FastSurferCNN/utils/arg_types.py
@@ -173,7 +173,7 @@ def int_ge_zero(value) -> int:
 
 def unquote_str(value) -> str:
     """
-    Unquote a (single quoted) string.
+    Unquote a (single quoted) string, i.e. remove one level of single-quotes.
 
     Parameters
     ----------
@@ -183,7 +183,7 @@ def unquote_str(value) -> str:
     Returns
     -------
     val : str
-        A string of the value without quoting with '''.
+        A string of the value without leading and trailing single-quotes.
     """
     val = str(value)
     if val.startswith("'") and val.endswith("'"):

diff --git a/FastSurferCNN/utils/common.py b/FastSurferCNN/utils/common.py
@@ -41,7 +41,6 @@
     "iterate",
     "NoParallelExecutor",
     "pipeline",
-    "removesuffix",
     "SubjectList",
     "SubjectDirectory",
 ]
@@ -190,20 +189,19 @@ def pipeline(
     ----------
     pool : Executor
         Thread pool executor for parallel execution.
-
-    func : Callable[[_Ti], _T] :
+    func : callable
         Function to use.
-
-    iterable : Iterable[_Ti]
+    iterable : Iterable
         Iterable containing input elements.
-
-    pipeline_size : int
-        Size of the processing pipeline (default is 1).
+    pipeline_size : int, default=1
+        Size of the processing pipeline.
 
     Yields
     ------
-    Iterator[Tuple[_Ti, _T]]
-        Yielding elements from iterable and corresponding results from func(element).
+    element : _Ti
+        Elements
+    _T
+        Results of func corresponding to element: func(element).
     """
     # do pipeline loading the next element
     from collections import deque
@@ -231,54 +229,23 @@ def iterate(
     Parameters
     ----------
     pool : Executor
-        Callable.
-    func : Iterable
+        The Executor object (dummy object to have a common API with pipeline).
+    func : callable
         Function to use.
-    iterable : Iterable[_Ti]
-        Iterable.
+    iterable : Iterable
+        Iterable to draw objects to process with func from.
 
     Yields
     ------
-     element : _Ti
+    element : _Ti
         Elements
     _T
-        Func(element).
+        Results of func corresponding to element: func(element).
     """
     for element in iterable:
         yield element, func(element)
 
 
-def removesuffix(string: str, suffix: str) -> str:
-    """
-    Remove  a suffix from a string.
-
-    Similar to string.removesuffix in PY3.9+.
-
-    Parameters
-    ----------
-    string : str
-        String that should be edited.
-    suffix : str
-        Suffix to remove.
-
-    Returns
-    -------
-    str
-        Input string with removed suffix.
-    """
-    import sys
-
-    if sys.version_info.minor >= 9:
-        # removesuffix is a Python3.9 feature
-        return string.removesuffix(suffix)
-    else:
-        return (
-            string[: -len(suffix)]
-            if len(suffix) > 0 and string.endswith(suffix)
-            else string
-        )
-
-
 class SubjectDirectory:
     """
     Represent a subject directory.
@@ -1012,7 +979,7 @@ def __getitem__(self, item: Union[int, str]) -> SubjectDirectory:
             # subject is always an absolute path (or relative to the working directory) ... of the input file
             subject = self._subjects[item]
             sid = (
-                os.path.basename(removesuffix(subject, self._remove_suffix))
+                os.path.basename(subject.removesuffix(self._remove_suffix))
                 if self._sid is None
                 else self._sid
             )