misc

src/scgenerator/cli/cli.py

@@ -147,9 +147,11 @@ def run_sim(args):
 def merge(args):
     path_trees = io.build_path_trees(Path(args.path))
 
-    if args.output_name is None:
+    output = env.output_path()
-        args.output_name = path_trees[0][-1][0].parent.name + " merged"
+    if output is None:
-    io.merge(args.output_name, path_trees)
+        output = path_trees[0][-1][0].parent.name + " merged"
+
+    io.merge(output, path_trees)
 
 
 def prep_ray():

src/scgenerator/initialize.py

@@ -519,15 +519,15 @@ def validate_config_sequence(*configs: os.PathLike) -> Tuple[Config, int]:
     """
     previous = None
     variables = set()
-    num = 1
+    repeat = 1
     for config in configs:
         if (p := Path(config)).is_dir():
             config = p / "initial_config.toml"
         dico = io.load_toml(config)
         previous = Config.from_bare(override_config(dico, previous))
-        num *= previous.repeat
+        repeat = previous.repeat
         variables |= {(k, tuple(v)) for k, v in previous.variable.items()}
-    return previous, num * int(np.product([len(v) for k, v in variables if len(v) > 0]))
+    return previous, repeat * int(np.product([len(v) for k, v in variables if len(v) > 0]))
 
 
 def wspace(t, t_num=0):

src/scgenerator/physics/simulate.py

@@ -6,7 +6,7 @@ from typing import Dict, List, Tuple, Type
 
 import numpy as np
 
-from .. import const, env, initialize, io, utils
+from .. import env, initialize, io, utils
 from ..errors import IncompleteDataFolderError
 from ..logger import get_logger
 from . import pulse
@@ -668,7 +668,7 @@ def run_simulation_sequence(
         prev = sim.sim_dir
     path_trees = io.build_path_trees(sim.sim_dir)
 
-    final_name = env.get(const.OUTPUT_PATH)
+    final_name = env.get(env.OUTPUT_PATH)
     if final_name is None:
         final_name = path_trees[0][-1][0].parent.name + " merged"
 

src/scgenerator/spectra.py

@@ -33,19 +33,29 @@ class Spectrum(np.ndarray):
 
 
 class Pulse(Sequence):
-    def __init__(self, path: os.PathLike, ensure_2d=True):
+    def __init__(self, path: os.PathLike, default_ind: Union[int, Iterable[int]] = None):
+        """load a data folder as a pulse
+
+        Parameters
+        ----------
+        path : os.PathLike
+            path to the data (folder containing .npy files)
+        default_ind : int | Iterable[int], optional
+            default indices to be loaded, by default None
+
+        Raises
+        ------
+        FileNotFoundError
+            path does not contain proper data
+        """
         self.logger = get_logger(__name__)
         self.path = Path(path)
-        self.__ensure_2d = ensure_2d
+        self.default_ind = default_ind
 
         if not self.path.is_dir():
             raise FileNotFoundError(f"Folder {self.path} does not exist")
 
-        self.params = None
-        try:
         self.params = io.load_params(self.path / "params.toml")
-        except FileNotFoundError:
-            self.logger.info(f"parameters corresponding to {self.path} not found")
 
         initialize.build_sim_grid_in_place(self.params)
 
@@ -173,8 +183,11 @@ class Pulse(Sequence):
         # Check if file exists and assert how many z positions there are
 
         if ind is None:
+            if self.default_ind is None:
                 ind = range(self.nmax)
-        elif isinstance(ind, int):
+            else:
+                ind = self.default_ind
+        if isinstance(ind, int):
             ind = [ind]
 
         # Load the spectra
@@ -184,7 +197,9 @@ class Pulse(Sequence):
         spectra = np.array(spectra)
 
         self.logger.debug(f"all spectra from {self.path} successfully loaded")
-
+        if len(ind) == 1:
+            return spectra[0]
+        else:
             return spectra
 
     def all_fields(self, ind=None):
@@ -196,7 +211,6 @@ class Pulse(Sequence):
         if i in self.cache:
             return self.cache[i]
         spec = np.load(self.path / SPECN_FN.format(i))
-        if self.__ensure_2d:
         spec = np.atleast_2d(spec)
         spec = Spectrum(spec, self.wl, self.params.repetition_rate)
         self.cache[i] = spec

src/scgenerator/utils/__init__.py

@@ -6,6 +6,7 @@ scgenerator module but some function may be used in any python program
 
 import itertools
 import multiprocessing
+import re
 import threading
 from collections import abc
 from copy import deepcopy
@@ -195,7 +196,7 @@ def format_variable_list(l: List[Tuple[str, Any]]):
 
 
 def branch_id(branch: Tuple[Path, ...]) -> str:
-    return "".join("".join(b.name.split()[2:-2]) for b in branch)
+    return "".join("".join(re.sub(r"id\d\S*num\d", "", b.name).split()[2:-2]) for b in branch)
 
 
 def format_value(value) -> str: