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Author: TimoK93

ctc_metrics/metrics/__init__.py

@@ -6,3 +6,13 @@
 from ctc_metrics.metrics.technical.seg import seg
 from ctc_metrics.metrics.technical.tra import tra
 from ctc_metrics.metrics.technical.det import det
+from ctc_metrics.metrics.technical.op_ctb import op_ctb
+from ctc_metrics.metrics.technical.op_csb import op_csb
+from ctc_metrics.metrics.biological.bio import bio
+from ctc_metrics.metrics.biological.op_clb import op_clb
+from ctc_metrics.metrics.technical.lnk import lnk
+
+ALL_METRICS = [
+    "Valid", "BC", "CT", "CCA", "TF", "SEG", "TRA", "DET", "LNK", "OP_CTB",
+    "OP_CSB", "BIO", "OP_CLB"
+]

ctc_metrics/metrics/biological/bio.py

@@ -0,0 +1,39 @@
+
+def bio(
+        ct: float,
+        tf: float,
+        bc: float,
+        cca: float,
+):
+    """
+    Computes the BIO. As described by
+        [celltrackingchallenge](http://celltrackingchallenge.net/).
+
+    Args:
+        ct: The complete tracking metric.
+        tf: The track fractions metric.
+        bc: The branching correctness metric.
+        cca: The cell cycle accuracy metric.
+
+    Returns:
+        The bio metric.
+    """
+    total_metrics = 0
+    if ct is not None:
+        total_metrics += 1
+    else:
+        ct = 0
+    if tf is not None:
+        total_metrics += 1
+    else:
+        tf = 0
+    if bc is not None:
+        total_metrics += 1
+    else:
+        bc = 0
+    if cca is not None:
+        total_metrics += 1
+    else:
+        cca = 0
+    bio = (ct + tf + bc + cca) / total_metrics
+    return bio

ctc_metrics/metrics/biological/op_clb.py

@@ -0,0 +1,19 @@
+
+def op_clb(
+        lnk: float,
+        bio: float,
+):
+    """
+    Computes the OP_CLB metric. As described by
+        [celltrackingchallenge](http://celltrackingchallenge.net/).
+
+    Args:
+        lnk: The linking metric.
+        bio: The biological metric.
+
+    Returns:
+        The OP_CLB metric.
+    """
+
+    op = 0.5 * lnk + 0.5 * bio
+    return op

ctc_metrics/metrics/technical/lnk.py

@@ -0,0 +1,37 @@
+
+def lnk(
+        ED: int,
+        EA: int,
+        EC: int,
+        num_edges: int,
+        **_ignored
+):
+    """
+    Calculate Linking (LNK) metric.
+
+    According to
+        Cell Tracking Accuracy Measurement Based on Comparison of Acyclic
+        Oriented Graphs; Matula etal. 2015
+
+    Args:
+        ED: Number of redundant edge.
+        EA: Number of missing edges.
+        EC: Number of wrong edge semantics.
+        num_edges: Number of edges in the graph.
+        _ignored: Ignored arguments.
+
+    Returns:
+        The Linking metric.
+    """
+    # Calculate AOGM_A
+    w_ed = 1
+    w_ea = 1.5
+    w_ec = 1
+    AOGM_A = w_ed * ED + w_ea * EA + w_ec * EC
+    # Calculate AOGM_0 (create graph from scratch)
+    #   i.e, all vertices and edges are false negatives
+    AOGM_0 = w_ea * num_edges
+    # Calculate DET
+    LNK = 1 - min(AOGM_A, AOGM_0) / AOGM_0
+    return float(LNK)
+

ctc_metrics/metrics/technical/op_csb.py

@@ -0,0 +1,19 @@
+
+def op_csb(
+        seg: float,
+        det: float,
+):
+    """
+    Computes the OP_CSB metric. As described by
+        [celltrackingchallenge](http://celltrackingchallenge.net/).
+
+    Args:
+        seg: The segmentation metric.
+        det: The detection metric.
+
+    Returns:
+        The OP_CSB metric.
+    """
+
+    op = 0.5 * seg + 0.5 * det
+    return op

ctc_metrics/metrics/technical/op_ctb.py

@@ -0,0 +1,19 @@
+
+def op_ctb(
+        seg: float,
+        tra: float,
+):
+    """
+    Computes the OP_CTB metric. As described by
+        [celltrackingchallenge](http://celltrackingchallenge.net/).
+
+    Args:
+        seg: The segmentation metric.
+        tra: The tracking metric.
+
+    Returns:
+        The OP_CTB metric.
+    """
+
+    op = 0.5 * seg + 0.5 * tra
+    return op