[ENH] Minor bugs (#73)

* bug if negative values for histogram

* nofullskullmask

Author: davidmeunier79

skullTo3d/nodes/skull.py

@@ -233,7 +233,7 @@ def calculate_mean(data):
     print("X max : ", np.max(X))
 
     print("Round X max : ", np.round(np.max(X)))
-    nb_bins = (np.rint(np.max(X)/sample_bins)).astype(int)
+    nb_bins = (np.rint((np.max(X) - np.min(X))/sample_bins)).astype(int)
     print("Nb bins: ", nb_bins)
 
     f.write("X shape : {}\n".format(X.shape))

skullTo3d/pipelines/skull_pipe.py

@@ -1778,51 +1778,43 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
     else:
 
         # align_ct_on_T1
-        align_ct_on_T1 = pe.Node(
+        aladin_CT_on_T1 = pe.Node(
             interface=RegAladin(),
-            name="align_ct_on_T1")
+            name="aladin_CT_on_T1")
 
-        align_ct_on_T1.inputs.rig_only_flag = True
+        aladin_CT_on_T1.inputs.rig_only_flag = True
 
         skull_ct_pipe.connect(
             inputnode, 'ct',
-            align_ct_on_T1, "flo_file")
+            aladin_CT_on_T1, "flo_file")
 
         skull_ct_pipe.connect(
             inputnode, "native_T1",
-            align_ct_on_T1, "ref_file")
+            aladin_CT_on_T1, "ref_file")
 
-        if "align_ct_on_T1_2" in params:
-
-            # align_ct_on_T1
-            align_ct_on_T1_2 = pe.Node(
-                interface=RegAladin(),
-                name="align_ct_on_T1_2")
+        # align_ct_on_T1
+        aladin_CT_on_T1_2 = pe.Node(
+            interface=RegAladin(),
+            name="aladin_CT_on_T1_2")
 
-            align_ct_on_T1_2.inputs.rig_only_flag = True
+        aladin_CT_on_T1_2.inputs.rig_only_flag = True
 
-            skull_ct_pipe.connect(
-                align_ct_on_T1, 'res_file',
-                align_ct_on_T1_2, "flo_file")
+        skull_ct_pipe.connect(
+            aladin_CT_on_T1, 'res_file',
+            aladin_CT_on_T1_2, "flo_file")
 
-            skull_ct_pipe.connect(
-                inputnode, "native_T1",
-                align_ct_on_T1_2, "ref_file")
+        skull_ct_pipe.connect(
+            inputnode, "native_T1",
+            aladin_CT_on_T1_2, "ref_file")
 
         # align_ct_on_stereo_T1
         align_ct_on_stereo_T1 = pe.Node(
             interface=RegResample(pad_val=0.0),
             name="align_ct_on_stereo_T1")
 
-        if "align_ct_on_T1_2" in params:
-            skull_ct_pipe.connect(
-                align_ct_on_T1_2, 'res_file',
-                align_ct_on_stereo_T1, "flo_file")
-
-        else:
-            skull_ct_pipe.connect(
-                align_ct_on_T1, 'res_file',
-                align_ct_on_stereo_T1, "flo_file")
+        skull_ct_pipe.connect(
+            aladin_CT_on_T1_2, 'res_file',
+            align_ct_on_stereo_T1, "flo_file")
 
         skull_ct_pipe.connect(
             inputnode, 'native_to_stereo_trans',

skullTo3d/utils/utils_params.py

@@ -2,7 +2,7 @@
 def update_skull_params(ssoft, params):
 
     if "noheadmask" in ssoft:
-        print("Found nohead in soft")
+        print("Found noheadmask in soft")
 
         if "skull_petra_pipe" in params:
             spp = params["skull_petra_pipe"]
@@ -62,7 +62,7 @@ def update_skull_params(ssoft, params):
 
     elif "noskullmask" in ssoft:
 
-        print("Found noskull in soft")
+        print("Found noskullmask in soft")
 
         if "skull_petra_pipe" in params:
             spp = params["skull_petra_pipe"]
@@ -105,6 +105,31 @@ def update_skull_params(ssoft, params):
                 print('deleting skullmask_ct_pipe')
                 del spp["skullmask_ct_pipe"]
 
+    elif "nofullskullmask" in ssoft:
+
+        print("Found nofullskullmask in soft")
+
+        if "skull_petra_pipe" in params:
+            spp = params["skull_petra_pipe"]
+
+            if "fullskullmask_petra_pipe" in spp:
+                print('deleting fullskullmask_petra_pipe')
+                del spp["fullskullmask_petra_pipe"]
+
+        if "skull_megre_pipe" in params:
+            smp = params["skull_megre_pipe"]
+
+            if "fullskullmask_megre_pipe" in smp:
+                print('deleting fullskullmask_megre_pipe')
+                del smp["fullskullmask_megre_pipe"]
+
+        if "skull_t1_pipe" in params:
+            spp = params["skull_t1_pipe"]
+
+            if "fullskullmask_t1_pipe" in spp:
+                print('deleting fullskullmask_t1_pipe')
+                del spp["fullskullmask_t1_pipe"]
+
     # if no brain seg mask, removed fullskullmask
     if "noseg" in ssoft or "prep" in ssoft:
 

workflows/params_segment_marmo_ants_4animal_skull.json

@@ -301,7 +301,7 @@
         "use_T2":
         {
         },
-        "align_ct_on_T1_2":
+        "aladin_CT_on_T1":
         {
         },
         "skullmask_ct_pipe":

workflows/params_segment_marmo_ants_quick_skull.json

@@ -299,7 +299,7 @@
         "use_T2":
         {
         },
-        "align_ct_on_T1_2":
+        "aladin_CT_on_T1":
         {
         },
         "skullmask_ct_pipe":

workflows/params_segment_marmo_ants_skull.json

@@ -304,7 +304,7 @@
         "use_T2":
         {
         },
-        "align_ct_on_T1_2":
+        "aladin_CT_on_T1":
         {
         },
         "skullmask_ct_pipe":

workflows/segment_skull.py

@@ -180,11 +180,14 @@ def create_main_workflow(cmd, data_dir, process_dir, soft, species, subjects,
     if 'prep' in ssoft:
         new_ssoft.remove('prep')
 
+    if 'noheadmask' in ssoft:
+        new_ssoft.remove('noheadmask')
+
     if 'noskullmask' in ssoft:
         new_ssoft.remove('noskullmask')
 
-    if 'noheadmask' in ssoft:
-        new_ssoft.remove('noheadmask')
+    if 'nofullskullmask' in ssoft:
+        new_ssoft.remove('nofullskullmask')
 
     if 'noseg' in ssoft:
         new_ssoft.remove('noseg')