Merge pull request #337 from arayabrain/feature/add-multisession-params

add multisession params

studio/app/optinist/wrappers/caiman/cnmf_multisession.py

@@ -44,6 +44,8 @@ def caiman_cnmf_multisession(
 
     Ain = reshaped_params.pop("Ain", None)
     roi_thr = reshaped_params.pop("roi_thr", None)
+
+    # mulisiession params
     n_reg_files = reshaped_params.pop("n_reg_files", 2)
     if n_reg_files < 2:
         raise Exception(f"Set n_reg_files to a integer value gte 2. Now {n_reg_files}.")
@@ -54,6 +56,13 @@ def caiman_cnmf_multisession(
         )
         reg_file_rate = 1.0
 
+    align_flag = reshaped_params.pop("align_flag", True)
+    max_thr = reshaped_params.pop("max_thr", 0)
+    use_opt_flow = reshaped_params.pop("use_opt_flow", True)
+    thresh_cost = reshaped_params.pop("thresh_cost", 0.7)
+    max_dist = reshaped_params.pop("max_dist", 10)
+    enclosed_thr = reshaped_params.pop("enclosed_thr", None)
+
     split_image_paths = images.split_image(output_dir, n_files=n_reg_files)
     n_split_images = len(split_image_paths)
 
@@ -97,7 +106,15 @@ def caiman_cnmf_multisession(
     dims = templates[0].shape
 
     spatial_union, assignments, matchings = register_multisession(
-        A=spatial, dims=dims, templates=templates
+        A=spatial,
+        dims=dims,
+        templates=templates,
+        align_flag=align_flag,
+        max_thr=max_thr,
+        use_opt_flow=use_opt_flow,
+        thresh_cost=thresh_cost,
+        max_dist=max_dist,
+        enclosed_thr=enclosed_thr,
     )
 
     reg_files = int(len(split_image_paths) * reg_file_rate)

studio/app/optinist/wrappers/caiman/params/cnmf_multisession.yaml

@@ -11,8 +11,6 @@ data_params:
 
 init_params:
   # Ain: null  # TBD: need to support 2D array type.
-  n_reg_files: 2 # number of files to be split.
-  reg_file_rate: 1.0  # threshold for the cell is detected in how many files
   K: 4
   gSig: [4, 4]
   ssub: 1
@@ -32,6 +30,18 @@ patch_params:
 merge_params:
   merge_thr: 0.85
 
+multisession_params:
+  # Following 2 parameters are optinist specific.
+  n_reg_files: 2 # number of files to be split.
+  reg_file_rate: 1.0  # threshold for the cell is detected in how many files
+  # Following parameters are from CaImAn register_multisession.
+  align_flag: True  # align the templates before matching
+  max_thr: 0  # max threshold parameter before binarization
+  use_opt_flow: True  # use dense optical flow to align templates
+  thresh_cost: 0.7  # maximum distance considered
+  max_dist: 10  # max distance between centroids
+  enclosed_thr: null  # float, if not None set distance to at most the specified value
+                      # when ground truth is a subset of inferred
 
 # ----------------------------------------
 # Advanced Parameters