From 57e9994e06425bfc70e3b14661c0916ce6889a8a Mon Sep 17 00:00:00 2001
From: arielleleon <54869022+arielleleon@users.noreply.github.com>
Date: Thu, 5 Dec 2024 12:23:48 -0800
Subject: [PATCH] 11 change json where epoch locations are pulled from (#12)

* Edited extraction.py

* Edited metadata.yml

* Update metadata.yml
---
 code/extraction.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/code/extraction.py b/code/extraction.py
index 14e4690..7add1a5 100644
--- a/code/extraction.py
+++ b/code/extraction.py
@@ -220,15 +220,15 @@ def bergamo_segmentation(motion_corr_fp: Path, session: dict, temp_dir: Path) ->
         path to motion corrected h5 file
     """
     motion_dir = motion_corr_fp.parent
-    tiff_stem_locs = next(motion_dir.glob("tiff_stem_locations.json"))
-    with open(tiff_stem_locs, "r") as j:
-        tiff_stem_locations = json.load(j)
+    epoch_loc_fp = next(motion_dir.glob("epoch_locations.json"))
+    with open(epoch_loc_fp, "r") as j:
+        epoch_locations = json.load(j)
     valid_epoch_stems = [
         i["output_parameters"]["tiff_stem"]
         for i in session["stimulus_epochs"]
         if i["stimulus_name"] != "2p photostimulation"
     ]
-    frame_locations = [tiff_stem_locations[i] for i in valid_epoch_stems]
+    frame_locations = [epoch_locations[i] for i in valid_epoch_stems]
     frames_length = sum([(i[1] - i[0] + 1) for i in frame_locations])
 
     return create_virtual_dataset(
@@ -236,6 +236,7 @@ def bergamo_segmentation(motion_corr_fp: Path, session: dict, temp_dir: Path) ->
     )
 
 
+
 def get_metdata(input_dir: Path) -> Tuple[dict, dict, dict]:
     """Get the session and data description metadata from the input directory