cleaning up and reorg

Author: Zymrael

NoiseFree/B1.mat

@@ -587,9 +587,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.2"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

NoiseFree/B2.mat

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 278,
+   "execution_count": 291,
    "id": "de8cfc1f-4230-411a-ab93-4a745e2e823b",
    "metadata": {},
    "outputs": [
@@ -74,7 +74,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 280,
+   "execution_count": 292,
    "id": "90092913-2d0d-492d-8f36-f82b4ce9512d",
    "metadata": {},
    "outputs": [],
@@ -508,7 +508,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 289,
+   "execution_count": 293,
    "id": "cb79649a-c95b-449a-b342-af57472ac99b",
    "metadata": {},
    "outputs": [
@@ -538,7 +538,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 290,
+   "execution_count": null,
    "id": "6c1000c6-0d81-4061-9192-dbf8d7f0157e",
    "metadata": {},
    "outputs": [
@@ -554,159 +554,6 @@
       "\u001b[0m\u001b[0;32m    478 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
       "\u001b[0m\n"
      ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  n\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "TypeError: only integer scalar arrays can be converted to a scalar index\n",
-      "> \u001b[0;32m/home/stefano/michael/diffeqml/bo-phases/src/alg/algorithms.py\u001b[0m(476)\u001b[0;36mget_output\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;32m    474 \u001b[0;31m        \u001b[0mout_ns\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNamespace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    475 \u001b[0;31m        \u001b[0;32mimport\u001b[0m \u001b[0mpdb\u001b[0m\u001b[0;34m;\u001b[0m \u001b[0mpdb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_trace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m--> 476 \u001b[0;31m        \u001b[0mout_ns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0midx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mtopk_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    477 \u001b[0;31m        \u001b[0mout_ns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0my\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0my\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0midx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mtopk_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    478 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  n\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "--Return--\n",
-      "None\n",
-      "> \u001b[0;32m/home/stefano/michael/diffeqml/bo-phases/src/alg/algorithms.py\u001b[0m(476)\u001b[0;36mget_output\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;32m    474 \u001b[0;31m        \u001b[0mout_ns\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNamespace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    475 \u001b[0;31m        \u001b[0;32mimport\u001b[0m \u001b[0mpdb\u001b[0m\u001b[0;34m;\u001b[0m \u001b[0mpdb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_trace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m--> 476 \u001b[0;31m        \u001b[0mout_ns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0midx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mtopk_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    477 \u001b[0;31m        \u001b[0mout_ns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0my\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0my\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0midx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0midx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mtopk_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m    478 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  n\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "TypeError: only integer scalar arrays can be converted to a scalar index\n",
-      "> \u001b[0;32m/home/stefano/michael/diffeqml/bo-phases/src/alg/algorithms.py\u001b[0m(62)\u001b[0;36mrun_algorithm_on_f\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;32m     60 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     61 \u001b[0;31m        \u001b[0;31m# Return execution path and output\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m---> 62 \u001b[0;31m        \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_output\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     63 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     64 \u001b[0;31m    \u001b[0;32mdef\u001b[0m \u001b[0mget_exe_path_crop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  out_ns.x\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "*** NameError: name 'out_ns' is not defined\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  n\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "--Return--\n",
-      "None\n",
-      "> \u001b[0;32m/home/stefano/michael/diffeqml/bo-phases/src/alg/algorithms.py\u001b[0m(62)\u001b[0;36mrun_algorithm_on_f\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;32m     60 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     61 \u001b[0;31m        \u001b[0;31m# Return execution path and output\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m---> 62 \u001b[0;31m        \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexe_path\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_output\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     63 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\u001b[0;32m     64 \u001b[0;31m    \u001b[0;32mdef\u001b[0m \u001b[0mget_exe_path_crop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  n\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "TypeError: only integer scalar arrays can be converted to a scalar index\n",
-      "None\n",
-      "> \u001b[0;32m/tmp/ipykernel_5365/1929019883.py\u001b[0m(1)\u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n",
-      "\u001b[0;32m----> 1 \u001b[0;31m\u001b[0mexepath_gt\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_gt\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0malgo_gt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_algorithm_on_f\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  self.get_output()\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "*** NameError: name 'self' is not defined\n"
-     ]
-    },
-    {
-     "name": "stdin",
-     "output_type": "stream",
-     "text": [
-      "ipdb>  c\n"
-     ]
-    },
-    {
-     "ename": "TypeError",
-     "evalue": "only integer scalar arrays can be converted to a scalar index",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [290]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m exepath_gt, output_gt \u001b[38;5;241m=\u001b[39m \u001b[43malgo_gt\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_algorithm_on_f\u001b[49m\u001b[43m(\u001b[49m\u001b[43mf\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/michael/diffeqml/bo-phases/src/alg/algorithms.py:62\u001b[0m, in \u001b[0;36mAlgorithm.run_algorithm_on_f\u001b[0;34m(self, f)\u001b[0m\n\u001b[1;32m     59\u001b[0m     x \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake_step(f)\n\u001b[1;32m     61\u001b[0m \u001b[38;5;66;03m# Return execution path and output\u001b[39;00m\n\u001b[0;32m---> 62\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexe_path, \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget_output\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/michael/diffeqml/bo-phases/src/alg/algorithms.py:476\u001b[0m, in \u001b[0;36mTopK.get_output\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    474\u001b[0m out_ns \u001b[38;5;241m=\u001b[39m Namespace()\n\u001b[1;32m    475\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpdb\u001b[39;00m; pdb\u001b[38;5;241m.\u001b[39mset_trace()\n\u001b[0;32m--> 476\u001b[0m out_ns\u001b[38;5;241m.\u001b[39mx \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexe_path\u001b[38;5;241m.\u001b[39mx[idx] \u001b[38;5;28;01mfor\u001b[39;00m idx \u001b[38;5;129;01min\u001b[39;00m topk_idx]\n\u001b[1;32m    477\u001b[0m out_ns\u001b[38;5;241m.\u001b[39my \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexe_path\u001b[38;5;241m.\u001b[39my[idx] \u001b[38;5;28;01mfor\u001b[39;00m idx \u001b[38;5;129;01min\u001b[39;00m topk_idx]\n\u001b[1;32m    479\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m out_ns\n",
-      "File \u001b[0;32m~/michael/diffeqml/bo-phases/src/alg/algorithms.py:476\u001b[0m, in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m    474\u001b[0m out_ns \u001b[38;5;241m=\u001b[39m Namespace()\n\u001b[1;32m    475\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mpdb\u001b[39;00m; pdb\u001b[38;5;241m.\u001b[39mset_trace()\n\u001b[0;32m--> 476\u001b[0m out_ns\u001b[38;5;241m.\u001b[39mx \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexe_path\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mx\u001b[49m\u001b[43m[\u001b[49m\u001b[43midx\u001b[49m\u001b[43m]\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m idx \u001b[38;5;129;01min\u001b[39;00m topk_idx]\n\u001b[1;32m    477\u001b[0m out_ns\u001b[38;5;241m.\u001b[39my \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mexe_path\u001b[38;5;241m.\u001b[39my[idx] \u001b[38;5;28;01mfor\u001b[39;00m idx \u001b[38;5;129;01min\u001b[39;00m topk_idx]\n\u001b[1;32m    479\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m out_ns\n",
-      "\u001b[0;31mTypeError\u001b[0m: only integer scalar arrays can be converted to a scalar index"
-     ]
     }
    ],
    "source": [