From 840881723c366fbc7302c83c6fccf4e466b769b2 Mon Sep 17 00:00:00 2001
From: Alexandre Blanc <alexandre.blanc@pasteur.fr>
Date: Fri, 11 Oct 2024 18:17:40 +0200
Subject: [PATCH] Change trx syntax in repository, fix larva indexing
---
src/pytrxmat/repository.py | 9 +++++----
tests/test_repository.py | 1 +
tests/test_trx.py | 12 ++++++++++--
3 files changed, 16 insertions(+), 6 deletions(-)
diff --git a/src/pytrxmat/repository.py b/src/pytrxmat/repository.py
index 5aa76f0..b53d4fd 100644
--- a/src/pytrxmat/repository.py
+++ b/src/pytrxmat/repository.py
@@ -1,5 +1,6 @@
from pathlib import Path
from typing import Dict, List
+import functools
from .trx import TRX
class DateTime:
@@ -10,7 +11,7 @@ class DateTime:
@property
def trx(self)->TRX:
- return TRX(self.path/'trx.mat')
+ return functools.partial(TRX, self.path/'trx.mat')
class Protocol:
def __init__(self, name:str, root:Path):
@@ -34,7 +35,7 @@ class Line:
self.name = name
self.root = root
assert(str(root.name) == name)
- self._protocols:Dict[str, Protocol] = {p.name:Protocol(p.name, p) for p in self.root.glob('p_*') if p.is_dir()}
+ self._protocols:Dict[str, Protocol] = {p.name:Protocol(p.name, p) for p in self.root.iterdir() if p.is_dir() and (p.name.startswith('p_') or p.name.startswith('ch_'))}
def __getitem__(self, protocol:str)->Protocol:
return self._protocols[protocol]
@@ -82,8 +83,8 @@ class Tracker:
class Repository:
- def __init__(self, root:Path, trackers:List[str]):
- self.root = root
+ def __init__(self, root, trackers:List[str]):
+ self.root = Path(root)
self._trackers:Dict[str, Tracker] = {t:Tracker(t, self.root/t) for t in trackers if (self.root/t in self.root.iterdir()) and (self.root/t).is_dir()}
def __getitem__(self, tracker:str)->Tracker:
diff --git a/tests/test_repository.py b/tests/test_repository.py
index 9ec407f..7ef2a91 100644
--- a/tests/test_repository.py
+++ b/tests/test_repository.py
@@ -52,5 +52,6 @@ def test_repository(root):
print(dt)
for trx in repo.trx():
print(trx)
+ print(trx())
print(repo['t1']['a@a']['p_0']['00000000_000000'].trx)
diff --git a/tests/test_trx.py b/tests/test_trx.py
index ef77bde..ad0f32a 100644
--- a/tests/test_trx.py
+++ b/tests/test_trx.py
@@ -65,11 +65,19 @@ def test_get_string_asarray_false(trx: TRX):
s = trx.get_string(['neuron', 'protocol'], asarray=False)
print(s)
+def test_larva_filtering(trx: TRX):
+ larvae = trx.get_as_array('numero_larva_num')
+ larva = larvae[0].item()
+ x = trx.get_as_array(['t', 'x_head'], l=[larva])[0]
+ print(x)
+
+
if __name__ == '__main__':
- trx = TRX('trx.mat')
+ trx = TRX('tests/trx.mat')
test_get_scalar_list_larvae(trx)
test_get_ts_list_larvae(trx)
test_get_ts_and_scalar(trx)
test_get_bunched_scalar(trx)
test_get_string(trx)
- test_get_string_asarray_false(trx)
\ No newline at end of file
+ test_get_string_asarray_false(trx)
+ test_larva_filtering(trx)
\ No newline at end of file
--
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