From e69a2587d84ca7e4252c7790f8cc6b52cbcd5eea Mon Sep 17 00:00:00 2001
From: Noe Brucy <noe.brucy@cea.fr>
Date: Mon, 22 Nov 2021 11:50:29 +0100
Subject: [PATCH] [sinks] update sinks reader to be compatible with new code

---
 studyprocessor.py | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/studyprocessor.py b/studyprocessor.py
index 83ef311..a895c55 100644
--- a/studyprocessor.py
+++ b/studyprocessor.py
@@ -252,9 +252,14 @@ class StudyProcessor(Aggregator, HDF5Container):
                 nb_sink = np.int(content[i].split("=")[1])
                 mass_sink = np.float(content[i + 1].split("=")[1])
                 time = np.float(content[i + 2].split("=")[1])
+                timekey = np.float(content[i + 2].split("=")[0])
                 series["nb_sink"][run].append(nb_sink)
                 series["mass_sink"][run].append(mass_sink)
+
+                if "[yr]" not in timekey:
+                    time *= self.info["unit_time"].express(U.yr)
                 series["time"][run].append(time)
+
             except (ValueError, IndexError):
                 self._log(
                     "Error encountered in parsing {} (grepped block {})".format(
@@ -392,8 +397,8 @@ class StudyProcessor(Aggregator, HDF5Container):
         """
         avg_window in year
         """
-        time_unit = self.save.get_node("/series/sinks_from_log/time")._v_attrs.unit
-        mass_unit = self.save.get_node("/series/sinks_from_log/mass_sink")._v_attrs.unit
+        time_unit = self.get_attribute("/series/sinks_from_log/time", "unit")
+        mass_unit = self.get_attribute("/series/sinks_from_log/mass_sink", "unit")
         ssfr = {}
         for run in self.runs:
             # Surface of the box in pc^2
@@ -401,11 +406,9 @@ class StudyProcessor(Aggregator, HDF5Container):
             surface = (info["unit_length"].express(U.pc)) ** 2
             # WARNING : We do not multiply by boxlen since already done in 'unit_length' (pymses)
 
-            time = self.save.get_node("/series/sinks_from_log/time/" + run).read()
+            time = self.get_value(f"/series/sinks_from_log/time/{run}")
             time = time * time_unit.express(U.year)
-            mass_sink = self.save.get_node(
-                "/series/sinks_from_log/mass_sink/" + run
-            ).read()
+            mass_sink = self.get_value(f"/series/sinks_from_log/mass_sink/{run}")
             mass_sink = mass_sink * mass_unit.express(U.Msun)
 
             if avg_window is None:
@@ -425,15 +428,13 @@ class StudyProcessor(Aggregator, HDF5Container):
         return ssfr, {"avg_window": avg_window}
 
     def _surfacic_sink_mass(self):
-        mass_unit = self.save.get_node("/series/sinks_from_log/mass_sink")._v_attrs.unit
+        mass_unit = self.get_attribute("/series/sinks_from_log/mass_sink", "unit")
         ssm = {}
         for run in self.runs:
             # Surface of the box in pc^2
             info = self.snaps[run][self.nums[run][0]].info
             surface = (info["unit_length"].express(U.pc)) ** 2
-            mass_sink = self.save.get_node(
-                "/series/sinks_from_log/mass_sink/" + run
-            ).read()
+            mass_sink = self.get_value(f"/series/sinks_from_log/mass_sink/{run}")
             mass_sink = mass_sink * mass_unit.express(U.Msun)
 
             ssm[run] = mass_sink / surface
@@ -443,11 +444,9 @@ class StudyProcessor(Aggregator, HDF5Container):
     def _turb_power(self):
         turb_power = {}
         for run in self.runs:
-            dt = self.save.get_node("/series/rms_from_log/dt/" + run).read()
+            dt = self.get_value("/series/rms_from_log/dt/{run}")
             # Energy injected at each timestep
-            energy = self.save.get_node(
-                "/series/rms_from_log/turb_energy/" + run
-            ).read()
+            energy = self.get_value("/series/rms_from_log/turb_energy/{run}")
             # Power of the turbulence at this step in Watts
             turb_power[run] = energy / dt
         return turb_power
@@ -563,7 +562,7 @@ class StudyProcessor(Aggregator, HDF5Container):
                     self._extract_sinks_from_log,
                 ),
                 group="/series",
-                unit={"time": "unit_time", "mass_sink": U.Msun, "nb_sink": U.none},
+                unit={"time": U.yr, "mass_sink": U.Msun, "nb_sink": U.none},
                 description={
                     "time": "Time",
                     "mass_sink": "Total mass of stars",