From 93f69ceb0647a7c6001a7753060026a241aad69b Mon Sep 17 00:00:00 2001 From: Sooyoung Cheong <64125280+c-sooyoung@users.noreply.github.com> Date: Sun, 16 Aug 2026 02:51:23 +0900 Subject: [PATCH] moved notebooks to sandbox --- notebooks/convergence.ipynb | 154 ------------------------------------ notebooks/mat_preview.ipynb | 127 ----------------------------- 2 files changed, 281 deletions(-) delete mode 100644 notebooks/convergence.ipynb delete mode 100644 notebooks/mat_preview.ipynb diff --git a/notebooks/convergence.ipynb b/notebooks/convergence.ipynb deleted file mode 100644 index 3a4d157..0000000 --- a/notebooks/convergence.ipynb +++ /dev/null @@ -1,154 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "65e78297", - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import numpy as np\n", - "import matplotlib.pyplot as plt" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "90917d29", - "metadata": {}, - "outputs": [], - "source": [ - "result_dir = \"../results/260812-Si/Si2V1_2\"\n", - "train_x = np.load(os.path.join(result_dir, 'train_x.npy')).T\n", - "train_y = np.load(os.path.join(result_dir, 'train_y.npy')).T\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "05c0f656", - "metadata": {}, - "outputs": [], - "source": [ - "train_x.shape" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "47b5dd69", - "metadata": {}, - "outputs": [], - "source": [ - "xparams = [\n", - " 'defocus [A]',\n", - " 'layers',\n", - " 'thickness [A]'\n", - "]\n", - "\n", - "sort_index = np.argsort(train_y)\n", - "\n", - "x = train_x[:,sort_index]\n", - "y = train_y[sort_index]\n", - "\n", - "EPSILON = 1e-3 # choose best according to plot\n", - "\n", - "train_y_scaled = np.log(-train_y + y[-1] + EPSILON)\n", - "y_scaled = np.log(-y + y[-1] + EPSILON)\n", - "\n", - "fig, ax = plt.subplots(1, 2, figsize=(7,3))\n", - "ax[0].plot(y, 'k')\n", - "ax[1].plot(y_scaled, 'k')\n", - "plt.show()\n", - "\n", - "fig, ax = plt.subplots(1, 2, figsize=(7,3))\n", - "ax[0].plot(train_y, 'k')\n", - "ax[1].plot(train_y_scaled, 'k')\n", - "plt.show()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4990770c", - "metadata": {}, - "outputs": [], - "source": [ - "cut = 0 # set to -1 to get all points\n", - "\n", - "fig, axs = plt.subplots(1, len(x), figsize=(3*len(x)+0.5, 3.5), sharey=True)\n", - "\n", - "for i, axi in enumerate(axs):\n", - " axi.scatter(x[i][cut:], y_scaled[cut:], c=y_scaled[cut:], cmap='coolwarm')\n", - " axi.set_xlabel(xparams[i])\n", - "\n", - "axs[0].set_ylabel('$- \\\\log (\\ \\\\mathtt{fourier\\_error}\\ )$')\n", - "\n", - "plt.tight_layout()\n", - "plt.show()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "a2694f3c", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "fig, axs = plt.subplots(len(x), len(x), figsize=(3*len(x)+0.5, 3*len(x)+0.5))\n", - "\n", - "for i, axi in enumerate(axs):\n", - " for j, axij in enumerate(axi):\n", - " axij.scatter(\n", - " x[j], x[i],\n", - " c = y_scaled, # color\n", - " cmap = 'coolwarm',\n", - " s = 20, # size\n", - " alpha = 0 if i == j else 1 # make diagonal transparent\n", - " )\n", - " if i == len(x)-1:\n", - " axij.set_xlabel(xparams[j])\n", - " else:\n", - " axij.set_xticks([])\n", - " if j == 0:\n", - " axij.set_ylabel(xparams[i])\n", - " else:\n", - " axij.set_yticks([])\n", - "\n", - "plt.tight_layout()\n", - "plt.show()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "295ca65c", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "lemon", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.12" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/notebooks/mat_preview.ipynb b/notebooks/mat_preview.ipynb deleted file mode 100644 index 059191c..0000000 --- a/notebooks/mat_preview.ipynb +++ /dev/null @@ -1,127 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 17, - "id": "5c8aa3fd", - "metadata": {}, - "outputs": [], - "source": [ - "from scipy.io import loadmat as scipy_loadmat\n", - "from mat73 import loadmat as mat73_loadmat\n", - "import numpy as np" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "1d3c8601", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'/home/swim/bo-ptycho/notebooks'" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "%pwd" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "4a419040", - "metadata": {}, - "outputs": [], - "source": [ - "f = \"/home/swim/Si_project/Si8V2_full/roi1_Ndp256/MLs_L1_p1_g64_Ndp192_pc1_noModel_Ns23_dz14.6087_reg0.2/Niter1000.mat\"" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "405b77b4", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "dict_keys(['__header__', '__version__', '__globals__', 'outputs', 'probe', 'object', 'p', '__function_workspace__'])" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "contents = scipy_loadmat(f)\n", - "contents.keys()" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "id": "8a7b58b2", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "mappingproxy({'object_ROI': (dtype('O'), 0),\n", - " 'binning': (dtype('O'), 8),\n", - " 'detector': (dtype('O'), 16),\n", - " 'dx_spec': (dtype('O'), 24),\n", - " 'lambda': (dtype('O'), 32),\n", - " 'multi_slice_param': (dtype('O'), 40),\n", - " 'obj_init_param': (dtype('O'), 48),\n", - " 'init_probe_file': (dtype('O'), 56),\n", - " 'normalize_init_probe': (dtype('O'), 64)})" - ] - }, - "execution_count": 25, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "contents['p'].dtype.fields" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d8870f98", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "lemon", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.12.12" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -}