few bug solving

baseprocessor.py

@@ -370,7 +370,7 @@ class HDF5Container(BaseProcessor):
             for base_unit_str in unit:
                 expo = unit[base_unit_str]
                 base_unit = self._get_units(base_unit_str)
-                new_unit = new_unit * base_unit ** expo
+                new_unit = new_unit * base_unit**expo
             return new_unit
         if (data is not None) and isinstance(data, dict) and list(unit)[0] in data:
             for key in unit:
@@ -435,7 +435,7 @@ class HDF5Container(BaseProcessor):
                         self._save_data(name_full + "/" + key, data[key], "", unit)
         else:
             try:
-                if len(data) == 0:
+                if data is None or len(data) == 0:
                     return
             except TypeError:
                 data = np.array([data])

snapshotprocessor.py

@@ -360,8 +360,11 @@ class SnapshotProcessor(HDF5Container):
 
         # Create selector object
         if selector is None:
+            dirpath = os.path.dirname(path)
+            if dirpath == "":
+                dirpath = "."
             selector = RunSelector(
-                os.path.dirname(path),
+                dirpath,
                 self.run,
                 self.num,
                 self.params.input.nml_filename,
@@ -452,9 +455,6 @@ class SnapshotProcessor(HDF5Container):
         if os.path.exists(part_filename):
             hydro_file = open(part_filename)
             part_file = open(f"{path}/output_{self.num:05}/part_file_descriptor.txt")
-            has_grav = os.path.exists(
-                f"{path}/output_{self.num:05}/grav_{self.num:05}.out00000"
-            )
             plines = part_file.readlines()
             part_var = np.unique(
                 list(map(lambda s: s.split(",")[1][1:].split("_")[0], plines[2:]))
@@ -463,7 +463,7 @@ class SnapshotProcessor(HDF5Container):
             part_var = []
 
         has_grav = os.path.exists(
-            f"{path}/output_{self.num:05}/grav_{self.num:05}.out00000"
+            f"{path}/output_{self.num:05}/grav_{self.num:05}.out00001"
         )
 
         def is_available(available_vars, pymsesrc, var):
@@ -684,12 +684,13 @@ class SnapshotProcessor(HDF5Container):
                 if len(data[key] > 0):
                     if f"/{group}/{key}" in hdf5 and overwrite:
                         hdf5.remove_node(f"/{group}/{key}")
-                    hdf5.create_array(
-                        f"/{group}", key, data[key], "", createparents=True
-                    )
-                    unit = self._get_units(self.unit_key[key])
-                    hdf5.get_node(f"/{group}/{key}").unit = unit
-                    nb_written += 1
+                    elif f"/{group}/{key}" not in hdf5:
+                        hdf5.create_array(
+                            f"/{group}", key, data[key], "", createparents=True
+                        )
+                        unit = self._get_units(self.unit_key[key])
+                        hdf5.get_node(f"/{group}/{key}").unit = unit
+                        nb_written += 1
                 else:
                     self.logger.warning("Empty key")
             if "namelist" not in hdf5.root._v_attrs:
@@ -747,7 +748,7 @@ class SnapshotProcessor(HDF5Container):
             self.cells = self.load_data(
                 cells_src,
                 filename,
-                True,
+                save,
                 keys=keys,
                 group="cells",
             )
@@ -1648,7 +1649,6 @@ class SnapshotProcessor(HDF5Container):
         outfile = self.pspec_filename
         if overwrite_file or not os.path.exists(self.pspec_filename):
             pspec.pspec(repo=self.path, iouts=[self.num], outfile=outfile, **kwargs)
-        return np.array([self.pspec_filename])
 
     def _write_particles(self):
         """Ensure particles are written in the hdf5 file"""

utils/convert_to_hdf5.py

@@ -1,8 +1,28 @@
 # coding: utf-8
 
+import argparse
+import os
 from snapshotprocessor import SnapshotProcessor
 
 
 def convert_to_hdf5(path, snap_num, path_out=".", filename=None, **kwargs):
     snap = SnapshotProcessor(path=path, num=snap_num, path_out=path_out, **kwargs)
     snap.convert_hdf5(filename)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Convert Ramses output into a list of cells"
+    )
+    parser.add_argument(
+        "snapshots", help="path to the snapshots", nargs="+", default=[]
+    )
+    parser.add_argument("-o", "--out", help="path to the output", default=".")
+
+    args = parser.parse_args()
+
+    for snap in args.snapshots:
+        path = os.path.dirname(snap)
+        numstem = os.path.basename(snap)
+        snap_num = int(numstem.split("_")[1])
+        convert_to_hdf5(path, snap_num, args.out)

utils/runselector.py

@@ -40,7 +40,7 @@ class NamelistRecursive:
 class RunSelector:
     def __init__(
         self,
-        path_in,
+        path_in=".",
         in_runs=None,
         in_nums="all",
         nml_filename="run.nml",
@@ -93,7 +93,7 @@ class RunSelector:
             sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
 
         """
-        
+
         # Initialize logger
         self.logger = logging.getLogger("run_self")
         self.logger.propagate = False
@@ -450,7 +450,9 @@ class RunSelector:
 
         # Be sure we have a namelist
         if self.fallback_nml and run not in self.namelist:
-            self.logger.warning(f"Used fallback namelist for run {run} from output {nums[0]}")
+            self.logger.warning(
+                f"Used fallback namelist for run {run} from output {nums[0]}"
+            )
             path = f"{self.path_in}/{run}/output_{nums[0]:05}/namelist.txt"
             self.namelist[run] = self.load_namelist(run, path=path)