From 697e804d4a289c934d4310db440bb5b28bb37ca8 Mon Sep 17 00:00:00 2001
From: Thinh Nguyen <thinh@vathes.com>
Date: Tue, 5 Sep 2023 22:16:28 -0500
Subject: [PATCH 1/2] add `validation` argument to dandi upload

---
 element_interface/dandi.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/element_interface/dandi.py b/element_interface/dandi.py
index 078e58a..22486b3 100644
--- a/element_interface/dandi.py
+++ b/element_interface/dandi.py
@@ -12,6 +12,7 @@ def upload_to_dandi(
     api_key: str = None,
     sync: bool = False,
     existing: str = "refresh",
+    validation: str = "required",
     shell=True,  # without this param, subprocess interprets first arg as file/dir
 ):
     """Upload NWB files to DANDI Archive
@@ -27,6 +28,7 @@ def upload_to_dandi(
         sync (str, optional): If True, delete all files in archive that are not present
             in the local directory.
         existing (str, optional): see full description from `dandi upload --help`
+        validation (str, optional): [require|skip|ignore] see full description from `dandi upload --help`
     """
 
     working_directory = working_directory or os.path.curdir
@@ -84,4 +86,5 @@ def upload_to_dandi(
         dandi_instance="dandi-staging" if staging else "dandi",
         existing=existing,
         sync=sync,
+        validation=validation,
     )

From b374a41c5029af32e3d1dda1f89460324ef881e9 Mon Sep 17 00:00:00 2001
From: Thinh Nguyen <thinh@datajoint.com>
Date: Thu, 12 Oct 2023 15:48:15 -0500
Subject: [PATCH 2/2] passing as argument to `fit_file`

---
 element_interface/run_caiman.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/element_interface/run_caiman.py b/element_interface/run_caiman.py
index 6cb1559..91913c4 100644
--- a/element_interface/run_caiman.py
+++ b/element_interface/run_caiman.py
@@ -35,6 +35,13 @@ def run_caiman(
     parameters["fnames"] = file_paths
     parameters["fr"] = sampling_rate
 
+    if "indicies" in parameters:
+        indices = params.pop("indicies")
+        indicies = slice(*indices[0]), slice(*indices[1])
+        parameters['motion'] = {**parameters.get('motion', {}), "indicies": indicies}
+    else:
+        indicies = None
+
     opts = params.CNMFParams(params_dict=parameters)
 
     c, dview, n_processes = cm.cluster.setup_cluster(
@@ -45,6 +52,7 @@ def run_caiman(
         cnm = CNMF(n_processes, params=opts, dview=dview)
         cnmf_output, mc_output = cnm.fit_file(
             motion_correct=True,
+            indices=indicies,
             include_eval=True,
             output_dir=output_dir,
             return_mc=True,