Merge branch 'dev'

docs/api/document.rst

@@ -1,21 +1,21 @@
-Document module
+Report module
 ============
 
-.. automodule:: vot.document
+.. automodule:: vot.report
    :members:
 
-.. automodule:: vot.document.common
+.. automodule:: vot.report.common
    :members:
 
-HTML document generation
+HTML report generation
 ------------------------
 
-.. automodule:: vot.document
+.. automodule:: vot.report
    :members:
 
-LaTeX document generation
+LaTeX report generation
 -------------------------
 
-.. automodule:: vot.document.latex
+.. automodule:: vot.report.latex
    :members:
 

vot/__init__.py

@@ -66,13 +66,24 @@ def check_updates() -> bool:
 from attributee import Attributee, Integer, Boolean
 
 class GlobalConfiguration(Attributee):
-    """Global configuration object for the toolkit. It is used to store global configuration options.
+    """Global configuration object for the toolkit. It is used to store global configuration options. It can be initialized
+    from environment variables. The following options are supported:
+
+    - ``VOT_DEBUG_MODE``: Enables debug mode for the toolkit.
+    - ``VOT_SEQUENCE_CACHE_SIZE``: Maximum number of sequences to keep in cache.
+    - ``VOT_RESULTS_BINARY``: Enables binary results format.
+    - ``VOT_MASK_OPTIMIZE_READ``: Enables mask optimization when reading masks.
+    - ``VOT_WORKER_POOL_SIZE``: Number of workers to use for parallel processing.
+    - ``VOT_PERSISTENT_CACHE``: Enables persistent cache for analysis results in workspace.
+
     """
 
     debug_mode = Boolean(default=False, description="Enables debug mode for the toolkit.")
-    sequence_cache_size = Integer(default=1000, description="Maximum number of sequences to keep in cache.")
+    sequence_cache_size = Integer(default=100, description="Maximum number of sequences to keep in cache.")
     results_binary = Boolean(default=True, description="Enables binary results format.")
     mask_optimize_read = Boolean(default=True, description="Enables mask optimization when reading masks.")
+    worker_pool_size = Integer(default=1, description="Number of workers to use for parallel processing.")
+    persistent_cache = Boolean(default=True, description="Enables persistent cache for analysis results in workspace.")
 
     def __init__(self):
         """Initializes the global configuration object. It reads the configuration from environment variables.
@@ -90,9 +101,7 @@ def __init__(self):
 
     def __repr__(self):
         """Returns a string representation of the global configuration object."""
-        return "debug_mode={} sequence_cache_size={} results_binary={} mask_optimize_read={}".format(
-            self.debug_mode, self.sequence_cache_size, self.results_binary, self.mask_optimize_read
-        )
+        return " ".join(["{}={}".format(k, getattr(self, k)) for k in self.attributes()])
 
 config = GlobalConfiguration()
 

vot/analysis/accuracy.py

@@ -34,6 +34,8 @@ def gather_overlaps(trajectory: List[Region], groundtruth: List[Region], burnin:
     Returns:
         np.ndarray: List of overlaps."""
 
+    assert len(trajectory) == len(groundtruth), "Trajectory and groundtruth must have the same length."
+
     overlaps = np.array(calculate_overlaps(trajectory, groundtruth, bounds))
     mask = np.ones(len(overlaps), dtype=bool)
 

vot/analysis/longterm.py

@@ -481,8 +481,8 @@ def _title_default(self):
 
     def describe(self):
         """Describes the analysis."""
-        return Measure("Non-reported Error", "NRE", 0, 1, Sorting.DESCENDING), \
-            Measure("Drift-rate Error", "DRE", 0, 1, Sorting.DESCENDING), \
+        return Measure("Non-reported Error", "NRE", 0, 1, Sorting.ASCENDING), \
+            Measure("Drift-rate Error", "DRE", 0, 1, Sorting.ASCENDING), \
             Measure("Absence-detection Quality", "ADQ", 0, 1, Sorting.DESCENDING),
 
     def subcompute(self, experiment: Experiment, tracker: Tracker, sequence: Sequence, dependencies: List[Grid]) -> Tuple[Any]:
@@ -562,8 +562,8 @@ def dependencies(self):
 
     def describe(self):
         """Describes the analysis."""
-        return Measure("Non-reported Error", "NRE", 0, 1, Sorting.DESCENDING), \
-            Measure("Drift-rate Error", "DRE", 0, 1, Sorting.DESCENDING), \
+        return Measure("Non-reported Error", "NRE", 0, 1, Sorting.ASCENDING), \
+            Measure("Drift-rate Error", "DRE", 0, 1, Sorting.ASCENDING), \
             Measure("Absence-detection Quality", "ADQ", 0, 1, Sorting.DESCENDING),
 
     def compatible(self, experiment: Experiment):

vot/analysis/tests.py

@@ -0,0 +1,24 @@
+""" Unit tests for analysis module. """
+
+
+import unittest
+
+class Tests(unittest.TestCase):
+    """ Unit tests for analysis module. """
+
+    def test_perfect_accuracy(self):
+        import numpy as np
+
+        from vot.region import Rectangle, Special
+        from vot.analysis.accuracy import gather_overlaps
+
+        trajectory = [Rectangle(0, 0, 100, 100)] * 30
+        groundtruth = [Rectangle(0, 0, 100, 100)] * 30
+
+        trajectory[0] = Special(1)
+
+        overlaps = gather_overlaps(trajectory, groundtruth)
+
+        print(overlaps)
+
+        self.assertEqual(np.mean(overlaps), 1)

vot/dataset/__init__.py

@@ -284,8 +284,7 @@ def append(self, image):
 
         self._images.append(image)
 
-    @property
-    def length(self) -> int:
+    def __len__(self) -> int:
         """Returns the length of the sequence channel in number of frames
         
         Returns:
@@ -868,11 +867,12 @@ def groundtruth(self, index=None):
         Returns:
             Region: Groundtruth region
         """
-        data = self.__preload()
-        if len(self.objects()) != 1:
+        objids = self.objects()
+
+        if len(objids) != 1:
             raise DatasetException("More than one object in sequence")
 
-        id = next(iter(data.objects))
+        id = next(iter(objids))
         return self.object(id, index)
 
     def tags(self, index: int = None) -> List[str]:
@@ -951,7 +951,7 @@ def __init__(self, name, channels):
         Raises:
             DatasetException: If images are not provided for all channels
         """
-        super().__init__(name, None)
+        super().__init__(name)
         self._channels = {c: InMemoryChannel() for c in channels}
         self._tags = {}
         self._values = {}
@@ -1014,7 +1014,8 @@ def channels(self) -> List[str]:
             List[str]: List of channel names
 
         """
-        return self._channels.keys()
+        print(self._channels.keys())
+        return set(self._channels.keys())
 
     def frame(self, index : int) -> "Frame":
         """Returns the specified frame. The frame is returned as a Frame object.
@@ -1133,15 +1134,14 @@ def size(self) -> tuple:
             tuple: Sequence size
         """
         return self.channel().size
-
-    @property
+
     def channels(self) -> list:
         """Returns a list of channel names 
         
         Returns:
             list: List of channel names
         """
-        return self._channels.keys()
+        return set(self._channels.keys())
 
 def download_bundle(url: str, path: str = "."):
     """Downloads a dataset bundle as a ZIP file and decompresses it.

vot/dataset/common.py

@@ -319,5 +319,11 @@ def write_sequence(directory: str, sequence: Sequence):
         with open(os.path.join(directory, "%s.value" % value), "w") as fp:
             fp.write(data)
 
-    write_trajectory(os.path.join(directory, "groundtruth.txt"), [f.groundtruth() for f in sequence])
+    # Write groundtruth in case of single object
+    if len(sequence.objects()) == 1:
+        write_trajectory(os.path.join(directory, "groundtruth.txt"), [f.groundtruth() for f in sequence])
+    else:
+        for id in sequence.objects():
+            write_trajectory(os.path.join(directory, "groundtruth_%s.txt" % id), [f.object(id) for f in sequence])
+
     write_properties(os.path.join(directory, "sequence"), metadata)

vot/dataset/proxy.py

@@ -26,7 +26,7 @@ def __len__(self):
         Returns:
             int: Length of the sequence.
         """
-        return len(self)
+        return len(self._source)
 
     def frame(self, index: int) -> Frame:
         """Returns a frame object for the given index. Forwards the request to the source sequence.
@@ -384,4 +384,27 @@ def groundtruth(self, index: int = None) -> List[Region]:
         Args:
             index (int): Index of the frame.
         """
-        return self._source.object(self._id, index)
+        return self._source.object(self._id, index)
+
+class ObjectsHideFilterSequence(ProxySequence):
+    """A proxy sequence that virtually removes specified objects from the sequence. Note that the object is not removed from the sequence, but only hidden when listing them.
+    """
+
+    def __init__(self, source: Sequence, ids: Set[str]):
+        """Creates an object hide filter proxy sequence.
+    
+        Args:
+            source (Sequence): Source sequence object
+            ids (Set[str]): IDs of the objects that will be hidden in the proxy sequence.
+        """
+        super().__init__(source)
+        self._ids = ids
+
+    def objects(self):
+        """Returns a dictionary of all objects in the sequence.
+        
+        Returns:
+            Dict[str, Object]: Dictionary of all objects in the sequence.
+        """
+        objects = self._source.objects()
+        return {id for id in objects if id not in self._ids}

vot/experiment/transformer.py

@@ -2,11 +2,11 @@
 
 import os
 from abc import abstractmethod
-from typing import List
+import typing
 
 from PIL import Image
 
-from attributee import Attributee, Integer, Float, Boolean
+from attributee import Attributee, Integer, Float, Boolean, String, List
 
 from vot.dataset import Sequence, InMemorySequence
 from vot.dataset.proxy import FrameMapSequence
@@ -28,7 +28,7 @@ def __init__(self, cache: "LocalStorage", **kwargs):
         self._cache = cache
 
     @abstractmethod
-    def __call__(self, sequence: Sequence) -> List[Sequence]:
+    def __call__(self, sequence: Sequence) -> typing.List[Sequence]:
         """Generate a list of sequences from the given sequence. The generated sequences are stored in the cache if needed.
 
         Args:
@@ -45,7 +45,7 @@ class SingleObject(Transformer):
 
     trim = Boolean(default=False, description="Trim each generated sequence to a visible subsection for the selected object")
 
-    def __call__(self, sequence: Sequence) -> List[Sequence]:
+    def __call__(self, sequence: Sequence) -> typing.List[Sequence]:
         """Generate a list of sequences from the given sequence.
         
         Args:
@@ -69,7 +69,7 @@ class Redetection(Transformer):
     padding = Float(default=2, val_min=0)
     scaling = Float(default=1, val_min=0.1, val_max=10)
 
-    def __call__(self, sequence: Sequence) -> List[Sequence]:
+    def __call__(self, sequence: Sequence) -> typing.List[Sequence]:
         """Generate a list of sequences from the given sequence.
         
         Args:
@@ -108,5 +108,21 @@ def __call__(self, sequence: Sequence) -> List[Sequence]:
             write_sequence(chache_dir, generated)
 
         source = read_sequence(chache_dir)
-        mapping = [0] * self.initialization + [1] * (len(self) - self.initialization)
+        mapping = [0] * self.initialization + [1] * (len(source) - self.initialization)
         return [FrameMapSequence(source, mapping)]
+
+@transformer_registry.register("ignore")
+class IgnoreObjects(Transformer):
+    """Transformer that hides objects with certain ids from the sequence."""
+
+    ids = List(String(), default=[], description="List of ids to be ignored")
+
+    def __call__(self, sequence: Sequence) -> typing.List[Sequence]:
+        """Generate a list of sequences from the given sequence.
+        
+        Args:
+            sequence (Sequence): The sequence to be transformed.
+        """
+        from vot.dataset.proxy import ObjectsHideFilterSequence
+
+        return [ObjectsHideFilterSequence(sequence, self.ids)]