some problem with overriding

src/scgenerator/cli/cli.py

@@ -74,6 +74,9 @@ def create_parser():
         "One plot is made for each limit set provided. Example : 600,1200,nm or -2,2,ps",
     )
     plot_parser.add_argument("--options", "-o", default=None)
+    plot_parser.add_argument(
+        "--show", action="store_true", help="show the plots instead of saving them"
+    )
     plot_parser.set_defaults(func=plot_all)
 
     dispersion_parser = subparsers.add_parser(
@@ -186,7 +189,7 @@ def plot_all(args):
     if args.options is not None:
         opts |= dict([o.split("=")[:2] for o in re.split("[, ]", args.options)])
     root = Path(args.sim_dir).resolve()
-    scripts.plot_all(root, args.spectrum_limits, **opts)
+    scripts.plot_all(root, args.spectrum_limits, show=args.show, **opts)
 
 
 def plot_init_field_spec(args):

src/scgenerator/plotting.py

@@ -13,6 +13,8 @@ from scipy.interpolate import UnivariateSpline
 from scipy.interpolate.interpolate import interp1d
 from tqdm import utils
 
+from scgenerator.const import PARAM_SEPARATOR
+
 from .logger import get_logger
 
 from . import io, math
@@ -65,7 +67,7 @@ def plot_setup(
 
     # ensure no overwrite
     ind = 0
-    while (full_path := (out_dir / (plot_name + f"_{ind}." + file_type))).exists():
+    while (full_path := (out_dir / (plot_name + f"{PARAM_SEPARATOR}{ind}." + file_type))).exists():
         ind += 1
 
     if mode == "default":
@@ -864,10 +866,11 @@ def uniform_axis(
     else:
         raise TypeError(f"Don't know how to interpret {new_axis_spec}")
     tmp_axis, ind, ext = units.sort_axis(axis, plt_range)
+    values = np.atleast_2d(values)
     if np.allclose((diff := np.diff(tmp_axis))[0], diff):
         new_axis = tmp_axis
+        values = values[:, ind]
     else:
-        values = np.atleast_2d(values)
         if plt_range.unit.type == "WL":
             values[:, ind] = np.apply_along_axis(units.to_WL, 1, values[:, ind], tmp_axis)
         new_axis = np.linspace(tmp_axis.min(), tmp_axis.max(), len(tmp_axis))

src/scgenerator/scripts/__init__.py

@@ -9,11 +9,12 @@ import numpy as np
 from tqdm import tqdm
 
 from ..utils.parameter import BareParams
+from ..const import PARAM_SEPARATOR
 
 from ..initialize import ParamSequence
 from ..physics import units, fiber
 from ..spectra import Pulse
-from ..utils import pretty_format_value, pretty_format_from_file_name, auto_crop
+from ..utils import pretty_format_value, pretty_format_from_sim_name, auto_crop
 from ..plotting import plot_setup
 from .. import env, math
 
@@ -24,7 +25,7 @@ def fingerprint(params: BareParams):
     return h1, h2
 
 
-def plot_all(sim_dir: Path, limits: list[str], **opts):
+def plot_all(sim_dir: Path, limits: list[str], show=False, **opts):
     for k, v in opts.items():
         if k in ["skip"]:
             opts[k] = int(v)
@@ -39,7 +40,12 @@ def plot_all(sim_dir: Path, limits: list[str], **opts):
             pulse = Pulse(p)
             for left, right, unit in limits:
                 path, fig, ax = plot_setup(
-                    pulse.path.parent / f"{pulse.path.name}_{left:.1f}_{right:.1f}_{unit}"
+                    pulse.path.parent
+                    / (
+                        pretty_format_from_sim_name(pulse.path.name)
+                        + PARAM_SEPARATOR
+                        + f"{left:.1f}{PARAM_SEPARATOR}{right:.1f}{PARAM_SEPARATOR}{unit}"
+                    )
                 )
                 pulse.plot_2D(
                     left,
@@ -49,8 +55,11 @@ def plot_all(sim_dir: Path, limits: list[str], **opts):
                     **opts,
                 )
                 bar.update()
-                fig.savefig(path, bbox_inches="tight")
-            plt.close("all")
+                if show:
+                    plt.show()
+                else:
+                    fig.savefig(path, bbox_inches="tight")
+                plt.close(fig)
 
 
 def plot_init_field_spec(

src/scgenerator/utils/__init__.py

@@ -208,15 +208,30 @@ def format_value(value) -> str:
 
 
 def pretty_format_value(name: str, value) -> str:
-    return getattr(BareParams, name).display(value)
+    try:
+        return getattr(BareParams, name).display(value)
+    except AttributeError:
+        return name + PARAM_SEPARATOR + str(value)
 
 
-def pretty_format_from_file_name(name: str) -> str:
+def pretty_format_from_sim_name(name: str) -> str:
+    """formats a pretty version of a simulation directory
+
+    Parameters
+    ----------
+    name : str
+        name of the simulation (directory name)
+
+    Returns
+    -------
+    str
+        prettier name
+    """
     s = name.split(PARAM_SEPARATOR)
     out = []
     for key, value in zip(s[::2], s[1::2]):
         try:
-            out.append(getattr(BareParams, key).display(float(value)))
+            out += [key.replace("_", " "), getattr(BareParams, key).display(float(value))]
         except (AttributeError, ValueError):
             out.append(key + PARAM_SEPARATOR + value)
     return PARAM_SEPARATOR.join(out)
@@ -307,6 +322,9 @@ def override_config(new: BareConfig, old: BareConfig = None) -> BareConfig:
         variable[k] = v
     for k in variable:
         new_dict[k] = None
+
+    new_dict["readjust_wavelength"] = False
+
     return replace(old, variable=variable, **new_dict)
 
 

src/scgenerator/utils/parameter.py

@@ -359,7 +359,7 @@ class BareParams:
     quantum_noise: bool = Parameter(boolean)
     shape: str = Parameter(literal("gaussian", "sech"))
     wavelength: float = Parameter(in_range_incl(100e-9, 3000e-9), display_info=(1e9, "nm"))
-    intensity_noise: float = Parameter(in_range_incl(0, 1))
+    intensity_noise: float = Parameter(in_range_incl(0, 1), display_info=(1e2, "%"))
     width: float = Parameter(in_range_excl(0, 1e-9), display_info=(1e15, "fs"))
     t0: float = Parameter(in_range_excl(0, 1e-9), display_info=(1e15, "fs"))
 

testing/test_new_iterator.py

@@ -1,14 +1,12 @@
 import scgenerator as sc
 from pathlib import Path
+import os
 
-p = Path("/Users/benoitsierro/Nextcloud/PhD/Supercontinuum/PCF Simulations/PPP")
+os.chdir("/Users/benoitsierro/Nextcloud/PhD/Supercontinuum/PCF Simulations/")
 
-configs = [
-    sc.io.load_config(p / c)
-    for c in ("PM1550.toml", "PMHNLF_appended.toml", "PM2000_appended.toml")
-]
+root = Path("PM1550+PMHNLF+PM1550+PM2000")
 
-for variable, params in sc.utils.required_simulations(*configs):
-    print(variable)
+confs = sc.io.load_config_sequence(root / "4_PM2000.toml")
+final = sc.utils.final_config_from_sequence(*confs)
 
-# sc.initialize.ContinuationParamSequence(configs[-1])
+print(final)