Merge pull request #114 from esa/release-0.1.1

Release 0.1.1

.gitignore

@@ -131,4 +131,5 @@ dmypy.json
 my_notebooks
 .vscode
 results
-cfg
+cfg
+notebooks/plots/

README.md

@@ -38,7 +38,7 @@ Neural Inverse Design of Nanostructures (NIDN) is a Python project by the Advanc
 
 <p align="center">
   <a href="https://github.com/esa/nidn">
-    <img src="docs/NIDN_Scheme_v2.drawio.drawio.png" alt="Scheme"  width="910" height="459">
+    <img src="docs/source/NIDN_Scheme_v2.drawio.drawio.png" alt="Scheme"  width="910" height="459">
   </a>
   <p align="center">
     Neural Inverse Design of Nanostructures with PyTorch
@@ -63,6 +63,10 @@ This project is based on:
 
 For more details than provided with NIDN on the forward models please refer to their docs. The adaptations of there code are in the folders [nidn/trcwa/](https://github.com/esa/NIDN/tree/main/nidn/trcwa) and [nidn/fdtd/](https://github.com/esa/NIDN/tree/main/nidn/fdtd).
 
+Below you can see results of an exemplary optimization of a three-uniform-layer material to design a 1150nm filter.
+
+![Exemplary optimization of a three-uniform-layer material to design a 1150nm filter. | width=300](/examples/BP-filter-3layer-opt.gif)
+![Exemplary optimization of a three-uniform-layer material to design a 1150nm filter. | width=300](/examples/BP-filter-3layer-eps.gif)
 <!-- GETTING STARTED -->
 
 ## Getting Started

docs/Makefile

@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
+SOURCEDIR     = source
 BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".

docs/make.bat

@@ -7,7 +7,7 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=.
+set SOURCEDIR=source
 set BUILDDIR=_build
 
 if "%1" == "" goto help

docs/conf.py → docs/source/conf.py

@@ -25,7 +25,7 @@
 author = "Pablo Gómez and Håvard Hem Toftevaag"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.0.1"
+release = "v0.1.1"
 
 
 # -- General configuration ---------------------------------------------------

nidn/plots/plot_eps_per_point.py

@@ -10,13 +10,17 @@
 from ..utils.global_constants import NIDN_FONTSIZE, NIDN_PLOT_COLOR_1
 
 
-def plot_eps_per_point(run_cfg, compare_to_material=None, save_path=None, legend=True):
+def plot_eps_per_point(
+    run_cfg, compare_to_material=None, save_path=None, legend=True, file_id=None
+):
     """This function plots the epsilon values of grid points against real materials. Optionally saves it.
 
     Args:
         run_cfg (dict): The run configuration.
         compare_to_material (str or list): Name(s) of the material to compare with. Available ones are in /materials/data.
         save_path (str, optional): Folder to save the plot in. Defaults to None, then the plot will not be saved.
+        legend (bool, optional): Whether to show layer legend
+        file_id (str, optional): Whether to add a postfix string
     """
     # Create epsilon grid from the model
     eps, _ = model_to_eps_grid(run_cfg.model, run_cfg)
@@ -147,4 +151,8 @@ def plot_eps_per_point(run_cfg, compare_to_material=None, save_path=None, legend
     fig.autofmt_xdate()
 
     if save_path is not None:
-        plt.savefig(save_path + "/eps_per_points.png", dpi=150)
+        plt.savefig(save_path + "/eps_per_points" + str(file_id) + ".png", dpi=150)
+        # fig.clf()
+        # plt.close(fig)
+    else:
+        plt.show()

nidn/plots/plot_epsilon_grid.py

@@ -61,3 +61,5 @@ def plot_epsilon_grid(eps, run_cfg, save_path=None):
 
     if save_path is not None:
         plt.savefig(save_path + "/eps_grid.png", dpi=150)
+    else:
+        plt.show()

nidn/plots/plot_losses.py

@@ -19,3 +19,6 @@ def plot_losses(run_cfg, save_path=None):
     plt.legend(["L1", "Loss", "Weighted Average Loss"])
     if save_path is not None:
         plt.savefig(save_path + "/losses.png", dpi=150)
+    else:
+        plt.show()
+

nidn/plots/plot_material_grid.py

@@ -114,3 +114,6 @@ def plot_material_grid(
 
     if save_path is not None:
         plt.savefig(save_path + "/material_grid.png", dpi=150)
+    else:
+        plt.show()
+

nidn/plots/plot_model_grid.py

@@ -20,7 +20,7 @@ def plot_model_grid(run_cfg, save_path=None):
 
     # Here we calculate the absolute value of the permittivity over all frequencies for each grid point
     eps = torch.mean(eps, dim=3)
-    eps = torch.sqrt(eps.real ** 2 + eps.imag ** 2)
+    eps = torch.sqrt(eps.real**2 + eps.imag**2)
 
     abs_values = eps.detach().cpu().numpy()
 
@@ -63,3 +63,5 @@ def plot_model_grid(run_cfg, save_path=None):
 
     if save_path is not None:
         plt.savefig(save_path + "/model_grid.png", dpi=150)
+    else:
+        plt.show()

nidn/plots/plot_model_grid_per_freq.py

@@ -88,3 +88,5 @@ def plot_model_grid_per_freq(run_cfg, freq_idx=[0, 1, 2, 3], save_path=None):
 
     if save_path is not None:
         plt.savefig(save_path + "/model_grid_per_freq.png", dpi=150)
+    else:
+        plt.show()

nidn/plots/plot_spectra.py

@@ -79,7 +79,7 @@ def plot_spectra(
     prod_T_spectrum=None,
     markers=True,
     filename=None,
-    ylim=[[0.0, 1.0],[0.0, 1.0]],
+    ylim=[[0.0, 1.0], [0.0, 1.0]],
 ):
     """Plots the produced RTA spectra together with the target spectra. Optionally saves it.
 
@@ -173,3 +173,7 @@ def plot_spectra(
             plt.savefig(save_path + "/spectra_comparison.png", dpi=150)
         else:
             plt.savefig(save_path + "/" + filename + ".png", dpi=300)
+        # fig.clf()
+        # plt.close(fig)
+    else:
+        plt.show()

nidn/plots/plot_spectrum.py

@@ -99,7 +99,7 @@ def plot_spectrum(
     #         max(max(A_spectrum), max(T_spectrum), max(R_spectrum)) + 0.1,
     #     ]
 
-    fig = plt.figure(figsize=(15, 5), dpi=300)
+    fig = plt.figure(figsize=(12, 4), dpi=150)
     fig.patch.set_facecolor("white")
 
     fig = _add_plot(
@@ -116,7 +116,7 @@ def plot_spectrum(
         target_frequencies,
         T_spectrum,
         ylimits,
-        (121 if not show_absorption else 132),
+        (122 if not show_absorption else 132),
         "Transmittance",
         markers=markers,
     )
@@ -138,3 +138,5 @@ def plot_spectrum(
             plt.savefig(save_path + "/spectrum.png", dpi=150)
         else:
             plt.savefig(save_path + "/" + filename + ".png", dpi=300)
+    else:
+        plt.show()

notebooks/FDTD_RCWA_TMM_Comparison.ipynb

@@ -183,19 +183,11 @@
     "    plt.ylim([-0.1,1.1])\n",
     "    plt.savefig(f'../results/{material}.png')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "140d2626",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.6 ('NIDN')",
+   "display_name": "Python 3.9.7 ('nidn')",
    "language": "python",
    "name": "python3"
   },
@@ -209,11 +201,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.9.7"
   },
   "vscode": {
    "interpreter": {
-    "hash": "f0a9101947082d57fdb1768cbb738b2d65701c74001bd4e9db965265346a5080"
+    "hash": "1ec5cfae9b828f8ab7e7cdcd8237afffb09b0704a5815a216abf273e6fa91aea"
    }
   }
  },

notebooks/Forward_Model_Simulation_with_FDTD.ipynb

@@ -70,7 +70,7 @@
     "# Choose FDTD method, TRCWA other option\n",
     "cfg.solver = \"FDTD\"\n",
     "# Set number of time steps in FDTD\n",
-    "cfg.FDTD_niter = 400\n",
+    "cfg.FDTD_niter = 600\n",
     "# Choose pulse type (continuous, hanning or ricker)\n",
     "cfg.FDTD_pulse_type = 'continuous'\n",
     "# Choose source type (line or point)\n",
@@ -160,7 +160,7 @@
     "#Largest wavelength\n",
     "cfg.physical_wavelength_range[1]=15e-7\n",
     "# Set number of time steps in FDTD\n",
-    "cfg.FDTD_niter = 800\n",
+    "cfg.FDTD_niter = 2400\n",
     "# Choose pulse type\n",
     "cfg.FDTD_pulse_type = 'continuous'"
    ]
@@ -217,7 +217,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.9.7 ('nidn')",
    "language": "python",
    "name": "python3"
   },
@@ -231,7 +231,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.10"
+   "version": "3.9.7"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "1ec5cfae9b828f8ab7e7cdcd8237afffb09b0704a5815a216abf273e6fa91aea"
+   }
   }
  },
  "nbformat": 4,