Remove depencency on Patrick's file, add wait option

pipeline_disk.py

@@ -1,11 +1,11 @@
 # coding: utf-8
 import sys
 import numpy as np
-import module_extract as me
-import extract_disk as d
 import pymses
 import os
+from shutil import copy
 import argparse
+import time
 import disk_postprocess as dp
 
 
@@ -24,19 +24,39 @@ parser.add_argument("-s", "--step", help="step between two output", type=int, de
 parser.add_argument(
     "-d", "--disk", help="do specific disk radial analysis", action="store_true"
 )
+parser.add_argument("-p", "--project", help="specify project name", default="disk")
+
+parser.add_argument(
+    "-w", "--watch", help="wait and watch for missing outputs", action="store_true"
+)
+parser.add_argument(
+    "-wt",
+    "--waiting_time",
+    help="time between to successive try when watching new outputs (in second)",
+    type=int,
+    default=120,
+)
+parser.add_argument(
+    "-af",
+    "--allowed_failures",
+    help="number of allowed failures when waiting",
+    default=30,
+)
+
 
 args = parser.parse_args()
 
 
 user = "nbrucy"
 folder = "simus"
-project = "disk"
+project = args.project
 runs = args.runs
 
 first = args.first_output
 last = args.last_output
 step = args.step
 
+
 for run in runs:
     path_suffix = user + "/" + folder + "/" + project + "/" + run
     path_in = storage_in + path_suffix
@@ -44,23 +64,32 @@ for run in runs:
 
     if not os.path.exists(path_out):
         os.makedirs(path_out)
+        copy(path_in + "/disk.nml", path_out)
+        copy(path_in + "/output_00001/compilation.txt", path_out)
 
     for i in range(first, last + 1, step):
-        me.make_image_zoom(
-            path_in,
-            i,
-            [0.5],
-            sinks=False,
-            force=False,
-            path_out=path_out,
-            tag=run + "_",
-            cpuamr=False,
-            mag_im=False,
-            AU_units=False,
-        )
-        # me.look(path_in, i)
-        if args.disk:
-            dp.disk_prop(
-                path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=True
-            )
-            dp.plot_disk_prop(path_out, i, tag=run + "_")
+        failures = 0
+        success = False
+
+        while not success:
+            try:
+                dp.make_image_disk(
+                    path_in, i, path_out=path_out, tag=run, map_size=1024
+                )
+                if args.disk:
+                    dp.disk_prop(
+                        path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=False
+                    )
+                    dp.plot_disk_prop(path_out, i, tag=run)
+                success = True
+            except ValueError:
+                if args.watch and failures < args.allowed_failures:
+                    failures = failures + 1
+                    print(
+                        "Unable to proceed for run {} output {}. Trying again in {} s ({} tries remaining)".format(
+                            run, i, args.waiting_time, args.allowed_failures - failures
+                        )
+                    )
+                    time.sleep(args.waiting_time)
+                else:
+                    raise