[misc] May last round of bug corrections

plotter.py

@@ -793,7 +793,7 @@ class Plotter(Aggregator, BaseProcessor):
                 except AttributeError:
                     cbar = plt.colorbar()
             if label is not None:
-                if text_embeded:
+                if colorbar_embeded:
                     cbar.set_label(" " + label, color=overtext_color, loc="bottom")
                 else:
                     cbar.set_label(label)
@@ -824,12 +824,11 @@ class Plotter(Aggregator, BaseProcessor):
                     plot_overlay = self.overlays[plot_overlay]
             xlim = plt.xlim()
             ylim = plt.ylim()
-            try:
+            if len(overlays_kwargs) > i:
                 plot_overlay(ax_los, im_extent, **overlays_kwargs[i])
-            except IndexError:
+            else:
                 plot_overlay(ax_los, im_extent)
-            finally:
+
-                # Restore previous limits in case overlays changed it
             plt.xlim(xlim)
             plt.ylim(ylim)
 

pspec_new.py

@@ -434,7 +434,7 @@ parser.add_argument(
     "repo", help="RAMSES output repository", type=str, default=".", nargs="?"
 )
 parser.add_argument(
-    "iouts", help="output numbers", type=args.selection, default=":", nargs="?"
+    "iouts", help="output numbers", type=int, default=[1], nargs="+"
 )
 parser.add_argument(
     "outfile",
@@ -520,7 +520,7 @@ def main(arg):
     iouts = arg.iouts  # tools.select_outputs(arg.repo, arg.iouts)
 
     for iout in iouts:
-        print("Output %d" % iout)
+        print(f"Output {iout}")
         print("Load data")
         read_lvl = None
         if True:
@@ -933,7 +933,7 @@ if __name__ == "__main__":
 
 
 def pspec(**kwargs):
-    arg = parser.parse_args("")
+    arg = parser.parse_args("1")
     for kwarg in kwargs:
         setattr(arg, kwarg, kwargs[kwarg])
     main(arg)

run_selector.py

@@ -56,8 +56,7 @@ class RunSelector:
         Select runs and outputs with several filter options.
         By default, all runs and outputs within path_in are considered
 
-        Parameters
+        Args:
-        ---------
 
             1. Define the set of runs and outputs considered
 
@@ -146,8 +145,8 @@ class RunSelector:
         """
         Sub-select runs and outputs from already selected runs and outputs
 
-        Parameters
+        Args:
-        ---------
+
             runs : str or list of str. The name runs to consider. Default: all.
             nums : int or list of int or str.
                 The output numbers to consider.
@@ -173,9 +172,7 @@ class RunSelector:
 
             sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
 
-        Returns
+        Returns:
-        -------
-
             (selected_runs, selected_nums)
         """
 
@@ -301,8 +298,7 @@ class RunSelector:
         """
         Select snapshots from the disk
 
-        Parameters
+        Args:
-        ---------
 
             in_nums : int or list of int or str.
                 The output numbers to consider.
@@ -382,7 +378,7 @@ class RunSelector:
             if position == "left":
                 return ileft
             elif position == "right":
-                return nums[iright]
+                return iright
             else:
                 dleft = np.abs(get_time(nums[ileft]) - time)
                 dright = np.abs(get_time(nums[iright]) - time)
@@ -457,3 +453,24 @@ class RunSelector:
             nums = list(filter(try_load_info, nums))
 
         return nums
+
+    def write_paths(self, prefix=None, filename="~/list_file"):
+        """ 
+        Write the paths of the selected runs on a file
+
+        Args:
+            prefix (str, optional): Prefix for the pathscd si. Defaults to path_in.
+            filename (str, optional): F. Defaults to "~/list_file".
+        """
+        if prefix is None:
+            prefix = self.path_in 
+        paths = []
+        for run in self.nums:
+            for num in nums[run]:
+                paths.append(f"{prefix}/{run}/output_{num:05}\n")
+        f = open(os.path.expanduser(filename), "w")
+        f.writelines(paths)
+        f.close()
+
+    
+

select_runs.py

@@ -2,10 +2,6 @@ from run_selector import RunSelector
 from plotter import Plotter, U
 import os
 
-path_from_home = "simus/ismfeed/allmode"
-names = "n6_st_2e5_seed3_T5Myr_nsink1e3_comp*"
-
-
 def prep_mcons(study):
     study.coarse_step_from_log()
 
@@ -18,12 +14,19 @@ def time_mcons(study, run, target=0.2):
     return time_target
 
 
-def find_nums(study, prep_function, time_function):
+def find_nums(study, prep_function, time_function, time_min=0):
+    """  
+    Once other filter are applied, select one output based on the time given by time function
+
+    Args:
+        prep_function (study:studyProcessor -> None): prepare a study object
+        time_function (study:studyProcessor, run:str -> time:float): compute selected time from the object 
+    """
     nums = {}
     prep_function(study)
     for run in study.runs:
-        time_target = time_function(study, run)
+        time_target = max(time_min, time_function(study, run))
-        rs = RunSelector(path_in=in_dir, in_runs=run, time=time_target, unit_time=U.Myr)
+        rs = RunSelector(path_in=study.path, in_runs=run, time_min=time_min, time=time_target, unit_time=U.Myr)
         nums.update(rs.nums)
     return nums
 
@@ -38,6 +41,10 @@ def write_paths(nums, path_from_home, filename="~/list_file"):
     f.close()
 
 
+if __name__ == '__main__':
+    path_from_home = "simus/ismfeed/allmode"
+    names = "n6_st_2e5_seed3_T5Myr_nsink1e3_comp*"
+
     in_dir = os.path.expanduser(f"~/{path_from_home}")
     study = Plotter(
         in_dir,
@@ -45,11 +52,5 @@ study = Plotter(
         nums="first",
         tag="select",
     ).study
-
-
     nums = find_nums(study, prep_mcons, time_mcons)
     write_paths(nums, ".")
-
-pl = Plotter(in_dir, runs=nums.keys(), nums=nums)
-
-pl.rho_pdf()

snapshotprocessor.py

@@ -1340,7 +1340,7 @@ class SnapshotProcessor(HDF5Container):
         second_line = f.readline()
         f.close()
 
-        if first_line[1] == "#":
+        if len(first_line) > 0 and first_line[1] == "#":
             header = first_line[3:-2].split(",")
             units = second_line[3:-2].split(",")
             df = pd.read_csv(csv_name, header=None, names=header, skiprows=2)

studyprocessor.py

@@ -269,7 +269,7 @@ class StudyProcessor(Aggregator, HDF5Container):
         return series
 
     def _extract_stellar_from_log(self, stellar_objects, log_filename, run):
-        cmd_grep = f"grep stellar {log_filename} -n"
+        cmd_grep = f"grep 'stellar objects:' {log_filename} -n"
         content = os.popen(cmd_grep).readlines()
         nb_stellar = list(map(lambda s: int(s.split()[1]), content))
         line_numbers = list(map(lambda s: int(s.split(":")[0]), content))
@@ -440,8 +440,13 @@ class StudyProcessor(Aggregator, HDF5Container):
 
     def get_coldens0(self, run):
         mp =  1.4 * 1.66 * 10**(-24) * U.g
+        try:
             z0 = self.get_nml("galbox_params/height0", run) * U.pc
             n0 = self.get_nml("galbox_params/dens0", run) * U.cm**(-3)
+        except KeyError:
+            z0 = self.get_nml("cloud_params/height0", run) * U.pc
+            n0 = self.get_nml("cloud_params/dens0", run) * U.cm**(-3)
+
         return (np.sqrt(2 * np.pi) * mp * z0 * n0).express(U.coldens)
 
     def total_mass(self):