LineageTree 1.8.0__py3-none-any.whl → 2.0.3__py3-none-any.whl

LineageTree/__init__.py

@@ -1,5 +1,30 @@
-__version__ = "1.8.0"
+__version__ = "2.0.3"
 from .lineageTree import lineageTree
 from .lineageTreeManager import lineageTreeManager
+from .loaders import (
+    read_from_ASTEC,
+    read_from_binary,
+    read_from_csv,
+    read_from_mamut_xml,
+    read_from_mastodon,
+    read_from_mastodon_csv,
+    read_from_tgmm_xml,
+    read_from_txt_for_celegans,
+    read_from_txt_for_celegans_BAO,
+    read_from_txt_for_celegans_CAO,
+)
 
-__all__ = (lineageTree, lineageTreeManager)
+__all__ = (
+    "lineageTree",
+    "lineageTreeManager",
+    "read_from_tgmm_xml",
+    "read_from_txt_for_celegans_BAO",
+    "read_from_ASTEC",
+    "read_from_binary",
+    "read_from_csv",
+    "read_from_mamut_xml",
+    "read_from_mastodon_csv",
+    "read_from_mastodon",
+    "read_from_txt_for_celegans",
+    "read_from_txt_for_celegans_CAO",
+)

LineageTree/legacy/export_csv.py

@@ -0,0 +1,70 @@
+import csv
+
+from lineageTree import lineageTree
+
+"""Writes a lineage tree into a series of csv files.
+
+ * spots.csv: id; label; timePoint; x; y; z; volume
+ * links.csv: source spot id; target spot id
+ * fates1.csv: tagValue
+ * fate_values1.csv: spot id; tagValue
+ * fates2.csv: tagValue
+ * fate_values2.csv: spot id; tagValue
+ * fates3.csv: tagValue
+ * fate_values3.csv: spot id; tagValue
+"""
+
+
+def export_to_csv():
+    tree = lineageTree("Astec-Pm10_properties.pkl", file_type="ASTEC")
+
+    spots = [["id", "label", "timePoint", "x", "y", "z", "volume"]]
+    for node_id in tree.nodes:
+        cell_name = tree["cell_name"].get(node_id, "unknown")
+        spots.append(
+            [
+                node_id,
+                cell_name,
+                tree.time.get(node_id),
+                tree.pos[node_id][0],
+                tree.pos[node_id][1],
+                tree.pos[node_id][2],
+                tree.volume[node_id],
+            ]
+        )
+    write("spots.csv", spots)
+
+    links = [["source", "target"]]
+    for edge in tree.edges:
+        links.append([edge[0], edge[1]])
+    write("links.csv", links)
+
+    write_fate(tree.fates, "fates1.csv", tree, "fate_values1.csv")
+    write_fate(tree["cell_fate_2"], "fates2.csv", tree, "fate_values2.csv")
+    write_fate(tree["cell_fate_3"], "fates3.csv", tree, "fate_values3.csv")
+
+
+def write_fate(fates, fate_name, tree, fate_value_name):
+    all_fates = []
+    for index in fates:
+        all_fates.append(fates[index])
+    unique_fates = set(all_fates)
+    fates_list = [["fate"]]
+    for fate in unique_fates:
+        fates_list.append([fate])
+    write(fate_name, fates_list)
+
+    fate_values = [["id", "value"]]
+    for node_id in tree.nodes:
+        fate_values.append([node_id, tree.fates.get(node_id)])
+    write(fate_value_name, fate_values)
+
+
+def write(file_path, data):
+    with open(file_path, mode="w", newline="") as file:
+        writer = csv.writer(file)
+        writer.writerows(data)
+
+
+if __name__ == "__main__":
+    export_to_csv()

LineageTree/legacy/to_lineajea.py

@@ -0,0 +1,30 @@
+import csv
+
+
+def write_csv_from_lT_to_lineaja(
+    lT, path_to, start: int = 0, finish: int = 300
+):
+    csv_dict = {}
+    for time in range(start, finish):
+        for node in lT.time_nodes[time]:
+            csv_dict[node] = {"pos": lT.pos[node], "t": time}
+    with open(path_to, "w", newline="\n") as file:
+        fieldnames = [
+            "time",
+            "positions_x",
+            "positions_y",
+            "positions_z",
+            "id",
+        ]
+        writer = csv.DictWriter(file, fieldnames=fieldnames)
+        writer.writeheader()
+        for node in csv_dict:
+            writer.writerow(
+                {
+                    "time": csv_dict[node]["t"],
+                    "positions_z": csv_dict[node]["pos"][0],
+                    "positions_y": csv_dict[node]["pos"][1],
+                    "positions_x": csv_dict[node]["pos"][2],
+                    "id": node,
+                }
+            )

LineageTree/legacy/to_motile.py

@@ -0,0 +1,36 @@
+import warnings
+
+from ..lineageTree import lineageTree
+
+try:
+    import motile
+except ImportError:
+    warnings.warn(
+        "No motile installed therefore you will not be able to produce links with motile.",
+        stacklevel=2,
+    )
+
+
+def to_motile(
+    lT: lineageTree, crop: int | None = None, max_dist=200, max_skip_frames=1
+):
+    try:
+        import networkx as nx
+    except ImportError:
+        raise Warning("Please install networkx")  # noqa: B904
+
+    fmt = nx.DiGraph()
+    if not crop:
+        crop = lT.t_e
+    for time in range(crop):
+        for time_node in lT.nodes_at_t(time):
+            fmt.add_node(
+                time_node,
+                t=lT.time[time_node],
+                pos=lT.pos[time_node],
+                score=1,
+            )
+
+    motile.add_cand_edges(fmt, max_dist, max_skip_frames=max_skip_frames)
+
+    return fmt