From 3ad3ed44dd093cc1d680dde23e2e4ed19dea3dc1 Mon Sep 17 00:00:00 2001 From: kushalbakshi Date: Tue, 23 Apr 2024 16:33:14 -0500 Subject: [PATCH 1/2] Check for bruker-generated multi_tiff --- element_interface/prairie_view_loader.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/element_interface/prairie_view_loader.py b/element_interface/prairie_view_loader.py index 6dcda90..9854a22 100644 --- a/element_interface/prairie_view_loader.py +++ b/element_interface/prairie_view_loader.py @@ -167,6 +167,7 @@ def _extract_prairieview_metadata(xml_filepath: str): bidirectional_scan = False # Does not support bidirectional roi = 0 + multi_tiff = xml_root.find(".//Sequence/Frame/File/[@page]") is not None recording_start_time = xml_root.find(".//Sequence/[@cycle='1']").attrib.get("time") # Get all channels and find unique values @@ -310,6 +311,7 @@ def _extract_prairieview_metadata(xml_filepath: str): frame_period=frame_period, bidirectional=bidirectional_scan, bidirectional_z=bidirection_z, + multi_tiff=multi_tiff, scan_datetime=scan_datetime, usecs_per_line=usec_per_line, scan_duration=total_scan_duration, From 1f3ab21e0621b0a7293185b6d37a5e31548df4a7 Mon Sep 17 00:00:00 2001 From: kushalbakshi Date: Tue, 4 Jun 2024 16:30:08 -0400 Subject: [PATCH 2/2] Update(run_caiman.py) use single thread to avoid multiprocessing error --- element_interface/run_caiman.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/element_interface/run_caiman.py b/element_interface/run_caiman.py index db6a059..5ca74d4 100644 --- a/element_interface/run_caiman.py +++ b/element_interface/run_caiman.py @@ -45,7 +45,7 @@ def run_caiman( opts = params.CNMFParams(params_dict=parameters) c, dview, n_processes = cm.cluster.setup_cluster( - backend="local", n_processes=None, single_thread=False + backend="local", n_processes=None, single_thread=True ) try: