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Solve naming issue in loader functions #75

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Merged
leoguignard merged 1 commit into from
Jun 16, 2025
Merged

Solve naming issue in loader functions #75

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16 changes: 8 additions & 8 deletions src/LineageTree/loaders.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,14 +146,14 @@ def read_from_csv(
id_, t, z, y, x, *_ = line
pred = None
t = int(t)
pos = np.array([x, y, z])
positions = np.array([x, y, z])
C = unique_id
corres[id_] = C
pos[-1] = pos[-1] * z_mult
positions[-1] = positions[-1] * z_mult
if pred in corres:
M = corres[pred]
successor.setdefault(M, []).append(C)
pos[C] = pos
pos[C] = positions
time[C] = t
if not name:
tmp_name = Path(file_path).stem
Expand Down Expand Up @@ -706,7 +706,7 @@ def read_from_tgmm_xml(
root = tree.getroot()
for unique_id, it in enumerate(root):
if "-1.#IND" not in it.attrib["m"] and "nan" not in it.attrib["m"]:
M_id, pos, cell_id, svIdx, lin_id = (
M_id, positions, cell_id, svIdx, lin_id = (
int(it.attrib["parent"]),
[float(v) for v in it.attrib["m"].split(" ") if v != ""],
int(it.attrib["id"]),
Expand All @@ -729,13 +729,13 @@ def read_from_tgmm_xml(
float(it.attrib["nu"]),
float(it.attrib["alphaPrior"]),
)
pos = np.array(pos)
positions = np.array(positions)
C = unique_id
pos[-1] = pos[-1] * z_mult
positions[-1] = positions[-1] * z_mult
if (t - 1, M_id) in time_id:
M = time_id[(t - 1, M_id)]
successor.setdefault(M, []).append(C)
pos[C] = pos
pos[C] = positions
time_id[(t, cell_id)] = C
time[C] = t
properties["svIdx"][C] = svIdx
Expand All @@ -745,7 +745,7 @@ def read_from_tgmm_xml(
tmp = list(np.array(W) * nu)
W[C] = np.array(W).reshape(3, 3)
properties["coeffs"][C] = (
tmp[:3] + tmp[4:6] + tmp[8:9] + list(pos)
tmp[:3] + tmp[4:6] + tmp[8:9] + list(positions)
)
if not name:
tmp_name = Path(file_format).stem
Expand Down
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