Merge branch 'master' of github.com:Macatools/macapype

Macatools · Mar 21, 2024 · 49a1547 · 49a1547
2 parents 8b0b285 + 70a1d9c
commit 49a1547
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Showing 8 changed files with 46 additions and 42 deletions.
diff --git a/macapype/utils/utils_params.py b/macapype/utils/utils_params.py
@@ -139,6 +139,27 @@ def update_preparation_params(ssoft=[], subjects=None, sessions=None,
                     using autocrop ")
 
                 extra_wf_name += "_crop_aladin"
+
+                if "robustreg" in ssoft and "crop_aladin_pipe" \
+                        in params["short_preparation_pipe"]:
+                    print("Using robustreg option")
+                    params["short_preparation_pipe"]["crop_aladin_pipe"] = {
+                        "reg_T1_on_template": {
+                            "nac_flag": True,
+                            "rig_only_flag": True,
+                            "nosym_flag": True,
+                            "ln_val": 12,
+                            "lp_val": 10,
+                            "smoo_r_val": 1.0
+                            },
+                        "reg_T1_on_template2": {
+                            "rig_only_flag": True,
+                            "nosym_flag": True,
+                            "ln_val": 17,
+                            "lp_val": 15,
+                            "smoo_r_val": 1.0
+                            }
+                        }
                 return params, indiv_params, extra_wf_name
 
             if prep_pipe == "short_preparation_pipe":
@@ -206,6 +227,27 @@ def update_params(ssoft=[], subjects=None, sessions=None,
                 print("Deleting crop_T1")
                 del params["short_preparation_pipe"]["crop_T1"]
 
+            if "robustreg" in ssoft and "crop_aladin_pipe" \
+                    in params["short_preparation_pipe"]:
+                print("Using robustreg option")
+                params["short_preparation_pipe"]["crop_aladin_pipe"] = {
+                    "reg_T1_on_template": {
+                        "nac_flag": True,
+                        "rig_only_flag": True,
+                        "nosym_flag": True,
+                        "ln_val": 12,
+                        "lp_val": 10,
+                        "smoo_r_val": 1.0
+                        },
+                    "reg_T1_on_template2": {
+                        "rig_only_flag": True,
+                        "nosym_flag": True,
+                        "ln_val": 17,
+                        "lp_val": 15,
+                        "smoo_r_val": 1.0
+                        }
+                    }
+
             print("New params after modification")
             pprint.pprint(params)
 

diff --git a/workflows/params_segment_baboon_ants.json b/workflows/params_segment_baboon_ants.json
@@ -8,23 +8,8 @@
         "aladin_T2_on_T1":{},
     	"crop_aladin_pipe":
     	{
-
             "reg_T1_on_template":
             {
-                "nac_flag": true,
-                "rig_only_flag":true,
-                "nosym_flag": true,
-                "ln_val" : 12,
-                "lp_val": 10,
-                "smoo_r_val" : 1.0
-            },
-            "reg_T1_on_template2":
-            {
-                "rig_only_flag":true,
-                "nosym_flag": true,
-                "ln_val" : 17,
-                "lp_val": 15,
-                "smoo_r_val" : 1.0
             },
             "crop_z_T1":
             {

diff --git a/workflows/params_segment_baboon_spm.json b/workflows/params_segment_baboon_spm.json
@@ -11,9 +11,6 @@
             "reg_T1_on_template":
             {
             },
-            "reg_T1_on_template2":
-            {
-            },
             "crop_z_T1":
             {
                 "brainsize": 70

diff --git a/workflows/params_segment_macaque_ants.json b/workflows/params_segment_macaque_ants.json
@@ -10,9 +10,6 @@
             "reg_T1_on_template":
             {
             },
-            "reg_T1_on_template2":
-            {
-            },
             "crop_z_T1":
             {
                 "brainsize": 70

diff --git a/workflows/params_segment_macaque_spm.json b/workflows/params_segment_macaque_spm.json
@@ -11,9 +11,6 @@
             "reg_T1_on_template":
             {
             },
-            "reg_T1_on_template2":
-            {
-            },
             "crop_z_T1":
             {
                 "brainsize": 70

diff --git a/workflows/params_segment_marmo_ants.json b/workflows/params_segment_marmo_ants.json
@@ -12,9 +12,6 @@
             "reg_T1_on_template":
             {
             },
-            "reg_T1_on_template2":
-            {
-            },
             "crop_z_T1":
             {
                 "brainsize": 30

diff --git a/workflows/params_segment_marmo_spm.json b/workflows/params_segment_marmo_spm.json
@@ -2,7 +2,7 @@
     "general":
     {
         "template_name": "MBM_v3.0.1",
-        "template_stereo_name": "bma-1_0p2mm_padded"
+        "template_stereo_name": "bma-1_0p2mm"
     },
      "short_preparation_pipe":
     {
@@ -11,20 +11,6 @@
     	{
             "reg_T1_on_template":
             {
-                "nac_flag": true,
-                "rig_only_flag": true,
-                "nosym_flag": true,
-                "ln_val": 12,
-                "lp_val": 10,
-                "smoo_r_val": 1.0
-            },
-            "reg_T1_on_template2":
-            {
-                "rig_only_flag": true,
-                "nosym_flag": true,
-                "ln_val": 17,
-                "lp_val": 15,
-                "smoo_r_val": 1.0
             },
             "crop_z_T1":
             {

diff --git a/workflows/segment_pnh.py b/workflows/segment_pnh.py
@@ -154,6 +154,9 @@ def create_main_workflow(data_dir, process_dir, soft, species, datatypes,
     if 'template' in ssoft:
         new_ssoft.remove('template')
 
+    if 'robustreg' in ssoft:
+        new_ssoft.remove('robustreg')
+
     soft = "_".join(new_ssoft)
 
     # formating args