From bf868c46684cca8060e89f4d00bfd9166ba21245 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Beno=C3=AEt=20Sierro?= <benoitsierro@bluewin.ch>
Date: Wed, 18 Aug 2021 09:56:02 +0200
Subject: [PATCH] changed default data directory path

---
 src/scgenerator/io.py               | 8 ++++----
 src/scgenerator/physics/pulse.py    | 2 +-
 src/scgenerator/physics/simulate.py | 7 +++++--
 src/scgenerator/utils/parameter.py  | 1 +
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/scgenerator/io.py b/src/scgenerator/io.py
index 33561cc..10fc8c9 100644
--- a/src/scgenerator/io.py
+++ b/src/scgenerator/io.py
@@ -454,12 +454,12 @@ def sim_dirs(path_trees: List[PathTree]) -> Generator[Path, None, None]:
         yield p[0].parent
 
 
-def get_sim_dir(task_id: int, name_if_new: str = "data") -> Path:
-    if name_if_new == "":
-        name_if_new = "data"
+def get_sim_dir(task_id: int, path_if_new: Path = None) -> Path:
+    if path_if_new is None:
+        path_if_new = Path("scgenerator data")
     tmp = env.data_folder(task_id)
     if tmp is None:
-        tmp = ensure_folder(Path("scgenerator" + PARAM_SEPARATOR + name_if_new))
+        tmp = ensure_folder(path_if_new)
         os.environ[TMP_FOLDER_KEY_BASE + str(task_id)] = str(tmp)
     tmp = Path(tmp).resolve()
     if not tmp.exists():
diff --git a/src/scgenerator/physics/pulse.py b/src/scgenerator/physics/pulse.py
index 2d6195a..8106282 100644
--- a/src/scgenerator/physics/pulse.py
+++ b/src/scgenerator/physics/pulse.py
@@ -739,7 +739,7 @@ def find_lobe_limits(x_axis, values, debug="", already_sorted=True):
         )
         ax.legend()
         fig.savefig(out_path, bbox_inches="tight")
-        plt.close(fig)
+        plt.close()
 
     else:
         good_roots, left_lim, right_lim = _select_roots(d_spline, d_roots, dd_roots, fwhm_pos)
diff --git a/src/scgenerator/physics/simulate.py b/src/scgenerator/physics/simulate.py
index 04f7eff..5c2837d 100644
--- a/src/scgenerator/physics/simulate.py
+++ b/src/scgenerator/physics/simulate.py
@@ -8,6 +8,7 @@ from typing import Dict, List, Tuple, Type, Union
 import numpy as np
 
 from .. import env, initialize, io, utils
+from ..const import PARAM_SEPARATOR
 from ..errors import IncompleteDataFolderError
 from ..logger import get_logger
 from . import pulse
@@ -438,7 +439,9 @@ class Simulations:
         self.update(param_seq)
 
         self.name = self.param_seq.name
-        self.sim_dir = io.get_sim_dir(self.id, name_if_new=self.name)
+        self.sim_dir = io.get_sim_dir(
+            self.id, path_if_new=Path(self.name + PARAM_SEPARATOR + "tmp")
+        )
         io.save_parameters(self.param_seq.config, self.sim_dir, file_name="initial_config.toml")
 
         self.sim_jobs_per_node = 1
@@ -690,7 +693,7 @@ def run_simulation_sequence(
 
     final_name = env.get(env.OUTPUT_PATH)
     if final_name is None:
-        final_name = path_trees[0][-1][0].parent.name + " merged"
+        final_name = config.name
 
     io.merge(final_name, path_trees)
 
diff --git a/src/scgenerator/utils/parameter.py b/src/scgenerator/utils/parameter.py
index 13e8983..b852a78 100644
--- a/src/scgenerator/utils/parameter.py
+++ b/src/scgenerator/utils/parameter.py
@@ -251,6 +251,7 @@ class VariableParameter:
 valid_variable = {
     "dispersion_file",
     "field_file",
+    "loss_file",
     "beta",
     "gamma",
     "pitch",