[misc] May last round of bug corrections

plotter.py

@@ -109,15 +109,15 @@ def quiver(ax, map_h, map_v, extent, key_v=None, label="", **kwargs):
     # add vector key
     if key_v is None:
         key_v = (max_v + min_v) / 2.0
-        ax.quiverkey(
+    ax.quiverkey(
-            vec_field,
+        vec_field,
-            0.6,
+        0.6,
-            0.98,
+        0.98,
-            key_v,
+        key_v,
-            f"${key_v:g}$ {label}",
+        f"${key_v:g}$ {label}",
-            labelpos="E",
+        labelpos="E",
-            coordinates="figure",
+        coordinates="figure",
-        )
+    )
 
 
 def line_integral_convolution(ax, map_h, map_v, extent, **kwargs):
@@ -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)
@@ -824,14 +824,13 @@ 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.xlim(xlim)
+            plt.ylim(ylim)
-                plt.ylim(ylim)
 
         return PlotInfo(
             plot_type=PlotType.IMAGE,

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

@@ -56,39 +56,38 @@ 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
+            1. Define the set of runs and outputs considered
 
-        path_in : str, path to the folder of the runs
+            path_in : str, path to the folder of the runs
 
-        2. Filter runs and outputs
+            2. Filter runs and outputs
 
-        in_runs : str or list of str. The name runs to consider. Default: all.
+            in_runs : str or list of str. The name runs to consider. Default: all.
-        in_nums : int or list of int or str.
+            in_nums : int or list of int or str.
-                  The output numbers to consider.
+                    The output numbers to consider.
-                  "last" select only the last output.
+                    "last" select only the last output.
-                  "all" preselect all outputs (default)
+                    "all" preselect all outputs (default)
 
-        nml_filename : str name of the namelist (should be the same for all outputs)
+            nml_filename : str name of the namelist (should be the same for all outputs)
 
-        filter_name : str, filter runs by name. Default "*"
+            filter_name : str, filter runs by name. Default "*"
-        filter_nml  : tuple or list of tupple.
+            filter_nml  : tuple or list of tupple.
-                     Filter runs by namelist.
+                        Filter runs by namelist.
-                     tuples are in the following form:
+                        tuples are in the following form:
-                     (nml_key, operator, nml_value)
+                        (nml_key, operator, nml_value)
-                     with nml_key a key from the namelist (eg. "cloud_params/dens0")
+                        with nml_key a key from the namelist (eg. "cloud_params/dens0")
-                     operator within ("=", "!=", "<", ">", "in")
+                        operator within ("=", "!=", "<", ">", "in")
-                     and nml_value a string, float or int
+                        and nml_value a string, float or int
-        time_min    : float, select output where time >= time_min (in code units)
+            time_min    : float, select output where time >= time_min (in code units)
-        time_max    : float, select output where time <= time_min (in code units)
+            time_max    : float, select output where time <= time_min (in code units)
-        time        : float or list of float. For each value, select the output closer to it.
+            time        : float or list of float. For each value, select the output closer to it.
-        unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
+            unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
 
-        3. Sort the runs
+            3. Sort the runs
 
-        sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
+            sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
 
         """
 
@@ -146,37 +145,35 @@ 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.
-             "last" select only the last output.
-             "all" preselect all outputs (default)
 
-        filter_name : str.
+            runs : str or list of str. The name runs to consider. Default: all.
-             glob pattern used to filter run names.
+            nums : int or list of int or str.
-             default is "*" (all runs)
+                The output numbers to consider.
+                "last" select only the last output.
+                "all" preselect all outputs (default)
 
-        filter_nml  : tuple or list of tupple.
+            filter_name : str.
-                     Filter runs by namelist.
+                glob pattern used to filter run names.
-                     tuples are in the following form:
+                default is "*" (all runs)
-                     (nml_key, operator, nml_value)
+
-                     with nml_key a key from the namelist (eg. "cloud_params/dens0")
+            filter_nml  : tuple or list of tupple.
-                     operator within ("=", "!=", "<", ">", "in")
+                        Filter runs by namelist.
-                     and nml_value a string, float or int
+                        tuples are in the following form:
-        time_min    : float, select output where time >= time_min (in code units)
+                        (nml_key, operator, nml_value)
-        time_max    : float, select output where time <= time_min (in code units)
+                        with nml_key a key from the namelist (eg. "cloud_params/dens0")
-        time        : float or list of float. For each value, select the output closer to it.
+                        operator within ("=", "!=", "<", ">", "in")
-        unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
+                        and nml_value a string, float or int
+            time_min    : float, select output where time >= time_min (in code units)
+            time_max    : float, select output where time <= time_min (in code units)
+            time        : float or list of float. For each value, select the output closer to it.
+            unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
 
 
-        sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
+            sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
 
-        Returns
+        Returns:
-        -------
+            (selected_runs, selected_nums)
-
-        (selected_runs, selected_nums)
         """
 
         if runs is None:
@@ -301,20 +298,19 @@ class RunSelector:
         """
         Select snapshots from the disk
 
-        Parameters
+        Args:
-        ---------
 
-        in_nums : int or list of int or str.
+            in_nums : int or list of int or str.
-             The output numbers to consider.
+                The output numbers to consider.
-             "last" select only the last output.
+                "last" select only the last output.
-             "all" preselect all outputs (default)
+                "all" preselect all outputs (default)
 
-        time_min    : float, select output where time >= time_min (in code units)
+            time_min    : float, select output where time >= time_min (in code units)
-        time_max    : float, select output where time <= time_min (in code units)
+            time_max    : float, select output where time <= time_min (in code units)
-        time        : float or list of float. For each value, select the output closer to it.
+            time        : float or list of float. For each value, select the output closer to it.
-        unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
+            unit_time   : astrophysix.Unit, unit for the time above. None is code unit.
 
-        do_tests    : test if the snapshots are actually on disk. Not needed when subselecting snapshots.
+            do_tests    : test if the snapshots are actually on disk. Not needed when subselecting snapshots.
         """
 
         # -- Initialize info loader --
@@ -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
 
@@ -38,18 +41,16 @@ def write_paths(nums, path_from_home, filename="~/list_file"):
     f.close()
 
 
-in_dir = os.path.expanduser(f"~/{path_from_home}")
+if __name__ == '__main__':
-study = Plotter(
+    path_from_home = "simus/ismfeed/allmode"
-    in_dir,
+    names = "n6_st_2e5_seed3_T5Myr_nsink1e3_comp*"
-    filter_name=names,
-    nums="first",
-    tag="select",
-).study
 
-
+    in_dir = os.path.expanduser(f"~/{path_from_home}")
-nums = find_nums(study, prep_mcons, time_mcons)
+    study = Plotter(
-write_paths(nums, ".")
+        in_dir,
-
+        filter_name=names,
-pl = Plotter(in_dir, runs=nums.keys(), nums=nums)
+        nums="first",
-
+        tag="select",
-pl.rho_pdf()
+    ).study
+    nums = find_nums(study, prep_mcons, time_mcons)
+    write_paths(nums, ".")

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
-        z0 = self.get_nml("galbox_params/height0", run) * U.pc
+        try:
-        n0 = self.get_nml("galbox_params/dens0", run) * U.cm**(-3)
+            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):