Return to a more complex executing scheme

bb_pipeline_tools/bb_pipeline_queue.py

@@ -35,7 +35,7 @@ class Usage(Exception):
 def choose_block(subject, runTopup, fileConfig, queue, coeff, num_shells,
                    b_value_shell, exec_block):
 
-    if ((exec_block == 0) or (exec_block == 123)):
+    if exec_block == 0:
         # Default value for job id. SGE does not wait for a job with this id.
         jobSTEP2 = "1"
         jobSTEP3 = "1"
@@ -45,15 +45,14 @@ def choose_block(subject, runTopup, fileConfig, queue, coeff, num_shells,
 
         if runTopup:
              jobSTEP2 = bb_pipeline_func(subject, jobSTEP1, fileConfig, queue, coeff)
-             jobSTEP3 = bb_pipeline_diff_joint(subject, jobSTEP1, fileConfig, queue,
+             jobSTEP3 = bb_pipeline_asl(subject, jobSTEP1, fileConfig)
+             jobSTEP4 = bb_pipeline_diff_joint(subject, jobSTEP1, fileConfig, queue,
                                                coeff, num_shells, b_value_shell,
                                                exec_block)
-             jobSTEP4 = bb_pipeline_asl(subject, jobSTEP1, fileConfig)
-
         jobSTEP5 = bb_pipeline_FS(subject, jobSTEP1, fileConfig, queue)
-        jobSTEP6 = bb_IDP(subject, str(jobSTEP1) + "," + str(jobSTEP2) + "," + str(jobSTEP3) + "," + str(jobSTEP4),
+        jobSTEP6 = bb_IDP(subject, str(jobSTEP1) + "," + str(jobSTEP2) + "," + str(jobSTEP4),
                           fileConfig, queue)
-        jobSTEP7 = bb_post_pipeline(subject, str(jobSTEP4) + "," + str(jobSTEP5) + "," + str(jobSTEP6),
+        jobSTEP7 = bb_post_pipeline(subject, str(jobSTEP3) + "," + str(jobSTEP5) + "," + str(jobSTEP6),
                                     fileConfig, queue)
 
         return jobSTEP7
@@ -67,30 +66,34 @@ def choose_block(subject, runTopup, fileConfig, queue, coeff, num_shells,
         else:
             return jobSTEP1
 
-    elif ((exec_block == 2) or (exec_block == 20)):
+    elif exec_block == 123:
+        jobSTEP1 = bb_pipeline_struct(subject, runTopup, fileConfig, queue, coeff)
         if runTopup:
-             jobSTEP2 = bb_pipeline_diff_joint(subject, 1, fileConfig, queue,
+             jobSTEP2 = bb_pipeline_func(subject, jobSTEP1, fileConfig, queue, coeff)
+             jobSTEP3 = bb_pipeline_asl(subject, jobSTEP1, fileConfig)
+             jobSTEP4 = bb_pipeline_diff_joint(subject, jobSTEP1, fileConfig, queue,
                                                coeff, num_shells, b_value_shell,
                                                exec_block)
-             return jobSTEP2
+             return jobSTEP4
         else:
-             return 1
-
-    elif (exec_block == 3):
-        jobSTEP1 = "1"
-        jobSTEP3 = "1"
-        jobSTEP4 = "1"
+            return jobSTEP1
 
+    elif ((exec_block == 2) or (exec_block == 20) or (exec_block == 3) or
+         (exec_block == 4) or (exec_block == 40)):
         if runTopup:
-             jobSTEP3 = bb_pipeline_diff_joint(subject, jobSTEP1, fileConfig, queue,
+             jobSTEP3 = bb_pipeline_diff_joint(subject, 1, fileConfig, queue,
                                                coeff, num_shells, b_value_shell,
                                                exec_block)
+             return jobSTEP3
+        else:
+             return 1
 
-        jobSTEP5 = bb_pipeline_FS(subject, jobSTEP1, fileConfig, queue)
-        jobSTEP6 = bb_IDP(subject, str(jobSTEP1) + "," + str(jobSTEP2) + "," + str(jobSTEP3) + "," + str(jobSTEP4),
-                          fileConfig, queue)
-        jobSTEP7 = bb_post_pipeline(subject, str(jobSTEP4) + "," + str(jobSTEP5) + "," + str(jobSTEP6),
-                                    fileConfig, queue)
+    if exec_block == 5:
+        jobSTEP5 = bb_pipeline_FS(subject, "1", fileConfig, queue)
+        jobSTEP6 = bb_IDP(subject, "1", fileConfig, queue)
+        jobSTEP7 = bb_post_pipeline(subject, str(jobSTEP5) + "," + str(jobSTEP6), fileConfig, queue)
+
+        return jobSTEP7
 
     else:
         return 1
@@ -153,12 +156,15 @@ def main():
                         dest="num_shells")
     parser.add_argument("-X", "--exec_block", action="store", nargs="?", default=0,
                         help='Pipeline block(s) to execute: Option (default 0): \n' +
-                             '  - 0   Run the whole pipeline with default parameters \n' +
-                             '  - 1   Run (CPU) 1st block (up until eddy) \n' +
-                             '  - 2   Run (GPU) 2nd block (eddy + bedpostX + probtrackX) \n' +
-                             '  - 3   Run (CPU) 3rd block (after eddy + bedpostX + probtrackX) \n' +
-                             '  - 20  Run (CPU) 2nd block (eddy + bedpostX + probtrackX) \n '+
-                             '  - 123 Run (CPU) 1st, 2nd, & 3rd block \n ',
+                             '  - 0: Run the whole pipeline with default parameters \n' +
+                             '  - 1: Run   (CPU) 1st block (up until eddy) \n' +
+                             '  - 2: Run   (GPU) 2nd block (eddy) \n' +
+                             '  - 3: Run   (CPU) 3rd block (after eddy, before bedpostX + probtrackX) \n' +
+                             '  - 4: Run   (GPU) 4th block (bedpostX + probtrackX) \n' +
+                             '  - 5: Run   (CPU) 5th block (everything after bedpostX + probtrackX) \n' +
+                             '  - 20: Run  (CPU) 2nd block (eddy) \n '+
+                             '  - 40: Run  (CPU) 4th block (bedpostX + probtrackX) \n ' +
+                             '  - 123: Run (CPU) 1st, 2nd, & 3rd block (up until bedpostX) \n ',
                         dest="exec_block")
 
     #########################
@@ -199,7 +205,6 @@ def main():
     if not os.path.exists(coeff):
         coeff = "none"
 
-
     # Parsing number of SWI coils argument
     if not argsa.coils_SWI:
         coils_SWI = 32
@@ -316,7 +321,7 @@ def main():
     else:
         try:
             exec_block = int(argsa.exec_block)
-            allowed_values = [0, 1, 2, 3, 20, 123]
+            allowed_values = [0, 1, 2, 3, 4, 5, 20, 40, 123]
 
             if not exec_block in allowed_values:
                 logger.warning("ERROR in the eXecute block: " +  exec_block +