Rename num_calls to num_samples

TODO.md

@@ -29,6 +29,7 @@ I2K 2022 *“developing open source image analysis platforms/tools”*
 - [x]  re-ordering channels
         np.ascontiguousarray, 'C' order, arr[..., (2, 1, 0)]
 - [x]  random sampling, shuffle in BatchDataLoader
+- [ ]  `indices` to index in hard-coded way for those that have no training/test split
 - [ ]  Metrics for benchmarking (StarDist has done a great job, their license is BSD-3)
 - [ ]  (maybe nope) Download scripts
 
@@ -51,8 +52,8 @@ I2K 2022 *“developing open source image analysis platforms/tools”*
         - [x]  BBBC041
 - [x]  consistent `root_dir`. Now it is a mess. We want something described in the
   `docs/user_guides/basic0_prepare_datasets.rst`.
+- [x]  substitute `num_calls` with `num_samples`? (I think samples sound right)
 - [ ]  number of images, including test sets
-- [ ]  substitute `num_calls` with `num_samples`? (I think samples sound right)
 - [ ]  Load all anno types, if there are more than one (e.g. BBBC007)
 
 ### Others

bioimageloader/base.py

@@ -82,7 +82,7 @@ class Dataset(DatasetInterface):
     root_dir
     output
     transforms
-    num_calls
+    num_samples
     grayscale : optional
     grayscale_mode : optional
     num_channels : optional
@@ -106,9 +106,9 @@ def __repr__(self):
         return self.acronym
 
     def __len__(self):
-        """Length of dataset. Can be overwritten with ``num_calls``"""
-        if self.num_calls is not None:
-            return self.num_calls
+        """Length of dataset. Can be overwritten with ``num_samples``"""
+        if self.num_samples is not None:
+            return self.num_samples
         return len(self.file_list)
 
     def __iter__(self):
@@ -136,10 +136,10 @@ def transforms(self) -> Optional[albumentations.Compose]:
         return None
 
     @property
-    def num_calls(self) -> Optional[int]:
+    def num_samples(self) -> Optional[int]:
         """Number of calls that will override __len__"""
-        if hasattr(self, '_num_calls'):
-            return getattr(self, '_num_calls')
+        if hasattr(self, '_num_samples'):
+            return getattr(self, '_num_samples')
         return None
 
     @property
@@ -189,15 +189,15 @@ def __getitem__(self, ind: int) -> Dict[str, np.ndarray]:
         Other Parameters
         ----------------
         self._transforms
-        self._num_calls
+        self._num_samples
         self._grayscale
         self._grayscale_mode
         self._num_channels
 
         """
-        # Randomize `ind` when `num_calls` set
-        if self.num_calls is not None:
-            if ind >= self.num_calls:
+        # Randomize `ind` when `num_samples` set
+        if self.num_samples is not None:
+            if ind >= self.num_samples:
                 raise IndexError('list index out of range')
             ind_max = len(self.file_list)
             ind = random.randrange(0, ind_max)
@@ -342,15 +342,15 @@ def __getitem__(self, ind: int) -> Dict[str, np.ndarray]:
         Other Parameters
         ----------------
         self._transforms
-        self._num_calls
+        self._num_samples
         self._grayscale
         self._grayscale_mode
         self._num_channels
 
         """
-        # Randomize `ind` when `num_calls` set
-        if self.num_calls is not None:
-            if ind >= self.num_calls:
+        # Randomize `ind` when `num_samples` set
+        if self.num_samples is not None:
+            if ind >= self.num_samples:
                 raise IndexError('list index out of range')
             ind_max = len(self.file_list)
             if (self.output != 'image') and (self.anno_dict is not None):

bioimageloader/collections/_bbbc002.py

@@ -25,7 +25,7 @@ class BBBC002(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
 
@@ -55,12 +55,12 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         **kwargs
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
 
     def get_image(self, p: Path) -> np.ndarray:
         img = tifffile.imread(p)

bioimageloader/collections/_bbbc006.py

@@ -35,7 +35,7 @@ class BBBC006(MaskDataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -81,7 +81,7 @@ def __init__(
         *,
         output: str = 'both',
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -92,7 +92,7 @@ def __init__(
         self._root_dir = root_dir
         self._output = output
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc007.py

@@ -33,7 +33,7 @@ class BBBC007(MaskDataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -76,7 +76,7 @@ def __init__(
         *,
         output: str = 'both',
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -87,7 +87,7 @@ def __init__(
         self._root_dir = root_dir
         self._output = output
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         self.image_ch = image_ch

bioimageloader/collections/_bbbc008.py

@@ -33,7 +33,7 @@ class BBBC008(MaskDataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when `transforms` is set. Define the total length of the dataset.
         If it is set, it overrides ``__len__``.
     grayscale : bool, default: False
@@ -74,7 +74,7 @@ def __init__(
         *,
         output: str = 'both',
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -85,7 +85,7 @@ def __init__(
         self._root_dir = root_dir
         self._output = output
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc013.py

@@ -27,7 +27,7 @@ class BBBC013(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -62,7 +62,7 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -71,7 +71,7 @@ def __init__(
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc014.py

@@ -32,7 +32,7 @@ class BBBC014(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -71,7 +71,7 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -80,7 +80,7 @@ def __init__(
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc015.py

@@ -33,7 +33,7 @@ class BBBC015(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -70,7 +70,7 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -79,7 +79,7 @@ def __init__(
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc016.py

@@ -30,7 +30,7 @@ class BBBC016(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -65,7 +65,7 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -74,7 +74,7 @@ def __init__(
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc018.py

@@ -39,7 +39,7 @@ class BBBC018(MaskDataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -101,7 +101,7 @@ def __init__(
         *,
         output: str = 'both',
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -113,7 +113,7 @@ def __init__(
         self._root_dir = root_dir
         self._output = output
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # self.image_ch = image_ch

bioimageloader/collections/_bbbc020.py

@@ -28,7 +28,7 @@ class BBBC020(MaskDataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -93,7 +93,7 @@ def __init__(
         *,
         output: str = 'both',
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # specific to this dataset
@@ -104,7 +104,7 @@ def __init__(
         self._root_dir = root_dir
         self._output = output
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         # specific to this dataset

bioimageloader/collections/_bbbc021.py

@@ -32,7 +32,7 @@ class BBBC021(Dataset):
     transforms : albumentations.Compose, optional
         An instance of Compose (albumentations pkg) that defines augmentation in
         sequence.
-    num_calls : int, optional
+    num_samples : int, optional
         Useful when ``transforms`` is set. Define the total length of the
         dataset. If it is set, it overwrites ``__len__``.
     grayscale : bool, default: False
@@ -72,7 +72,7 @@ def __init__(
         root_dir: str,
         *,
         transforms: Optional[albumentations.Compose] = None,
-        num_calls: Optional[int] = None,
+        num_samples: Optional[int] = None,
         grayscale: bool = False,
         grayscale_mode: Union[str, Sequence[float]] = 'equal',
         # # specific to this dataset
@@ -81,7 +81,7 @@ def __init__(
     ):
         self._root_dir = root_dir
         self._transforms = transforms
-        self._num_calls = num_calls
+        self._num_samples = num_samples
         self._grayscale = grayscale
         self._grayscale_mode = grayscale_mode
         self.image_ch = image_ch