changes README to reference repo of the actual parser

README.md

@@ -1,3 +1,5 @@
-# parser-eLabFTW-2-NeXus
+# parser-eLabFTW-jupyter
 
-Parser for eLabFTW to convert JSON data from the experiments to NeXus-compliant HDF5 files.
+Jupyter notebook collection to develop a parser for eLabFTW which is supposed to convert JSON data from the experiments to NeXus files for PLD depositions.
+
+Previously this repo was dedicated to the entire project. That is now: [emanuele/parser-eLabFTW-NFFA-DI](https://gitea.damico.ing/emanuele/parser-eLabFTW-NFFA-DI).

jupyter/chained_requests.ipynb

@@ -147,15 +147,15 @@
    "source": [
     "### Fetch any experiment related to a certain sample\n",
     "Another easy task is fetching every experiment entry related to a given sample. \\\n",
-    "Let's start with the sample of elabid equal to *1077* - which at the time I'm writing this is named \"Na-26-001 LMNO LAO\". The related experiments are Experiment 48 (layer 1) and Experiment 49 (layer 2). From these experiments we will only fetch *deposition time* and *repetition rate* to keep the present notebook clean.\n",
+    "Let's start with the sample of elabid equal to *1108* - which at the time I'm writing this is named \"Na-26-005\". The related experiments are Experiment 48 (layer 1) and Experiment 49 (layer 2). From these experiments we will only fetch *deposition time* and *repetition rate* to keep the present notebook clean.\n",
     "\n",
     "#### How linked experiments are managed by eLabFTW\n",
-    "Linked experiments are similar to linked items: you can reference an eLabFTW experiment into a resource, but when you download the data of the latter from the API endpoint you only get the elabid and **very few additional data** - like the experiment's title - of the former. In this situation the experiments linked to a sample contain information about its layers, which is at least level-1 nested since it requires at least an additional HTTP request."
+    "Linked experiments are similar to linked items: you can reference an eLabFTW experiment into a resource, but when you download the data of the latter from the API endpoint you only get the elabid and **very few additional data** - like the experiment's category - of the former. In this situation the experiments linked to a sample contain information about its layers, which is at least level-1 nested since it requires at least an additional HTTP request."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 8,
    "id": "504c6eec-967b-4886-8770-67b5df3ed5ef",
    "metadata": {},
    "outputs": [
@@ -169,11 +169,19 @@
     {
      "data": {
       "text/plain": [
-       "[{'deposition_time': '65', 'repetition_rate': '1'},\n",
-       " {'deposition_time': '56', 'repetition_rate': '1'}]"
+       "[{'title': 'Na-26-005',\n",
+       "  'layer_number': '1',\n",
+       "  'category': 'PLD Deposition',\n",
+       "  'deposition_time': '100',\n",
+       "  'repetition_rate': '1'},\n",
+       " {'title': 'Na-26-005 I',\n",
+       "  'layer_number': '2',\n",
+       "  'category': 'PLD Deposition',\n",
+       "  'deposition_time': '30',\n",
+       "  'repetition_rate': '1'}]"
       ]
      },
-     "execution_count": 18,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -202,21 +210,37 @@
     "        ).json()\n",
     "        extra = experiment_data[\"metadata_decoded\"][\"extra_fields\"]\n",
     "        result.append(\n",
-    "            {\"deposition_time\": extra.get(\"Duration\").get(\"value\"),\n",
+    "            {\"title\": exp.get(\"title\"),\n",
+    "             \"layer_number\": extra.get(\"Layer Progressive Number\").get(\"value\"),\n",
+    "             \"category\": exp.get(\"category_title\"),\n",
+    "             \"deposition_time\": extra.get(\"Duration\").get(\"value\"),\n",
     "             \"repetition_rate\": extra.get(\"Repetition rate\").get(\"value\")}\n",
     "        )\n",
     "    return result\n",
     "\n",
     "apikey = getpass(\"Paste API key here: \")\n",
-    "get_sample_layers_data(1077)"
+    "get_sample_layers_data(1108)"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "id": "046f7383-5830-462b-9ac0-2026e46c5697",
    "metadata": {},
-   "outputs": [],
+   "source": [
+    "The variables in the previous code can be best summarized as follows.\n",
+    "\n",
+    "* `related_experiments` (dict) only contains all of the linked experiments' elabid's, categories and titles.\n",
+    "* `experiment_data` (dict) contains ALL data related to one experiment at a time.\n",
+    "* `extra` (dict) is a sub-dictionary of `experiment_data` only containing the extra fields' values.\n",
+    "* The N-th item of `result` (list) contains cherrypicked data on the N-th layer.\n",
+    "\n",
+    "> ⚠️ The index of a layer in the `result` list does not necessarily equate the layer's progressive number."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2ca38bf4-ac33-481f-9ee2-99ec4db1686c",
+   "metadata": {},
    "source": []
   }
  ],
@@ -236,7 +260,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

requirements.txt

@@ -1,4 +1 @@
-numpy
-h5py>=3.15.1
-h5json>=1.1.3
-six
+notebook