main now turns content of realtime window analysis into nx dataset

the data is not parsed or analysed, it's written as text (well, tsv
technically) - this is only for testing and first attempts

src/functions.py

@@ -1,62 +0,0 @@
-"""
-Currently unused!
-"""
-import json, requests
-from APIHandler import APIHandler
-
-def get_entry_from_elabid(elabid, entryType="items"):
-    '''
-    Function which returns entrypoint data (as dictionary) from its elabid.
-    '''
-    header = APIHandler(apikey).dump
-    response = requests.get(
-        headers = header,
-        url = f"{ELABFTW_API_URL}/{entryType}/{elabid}",
-        verify=True
-    )
-    if response.status_code // 100 in [2,3]:
-        entry_data = response.json()
-        return entry_data
-    else:
-        raise ConnectionError(f"HTTP request failed with status code: {response.status_code}.")
-
-def get_sample_layers_data(elabid):
-    '''
-    Return the following data from every eLabFTW experiment linked
-    to a certain sample, identified by elabid.
-
-    - Title of the experiment
-    - Category (should check it's "PLD Deposition")
-    - Layer number - if present (PLD depositions)
-    - Deposition time - returns error if not present
-    - Repetition rate - returns error if not present
-    '''
-    # header = {
-    #     "Authorization": apikey,
-    #     "Content-Type": "application/json"
-    # }
-    sample_data = requests.get(
-        headers = header,
-        url = f"https://elabftw.fisica.unina.it/api/v2/items/{elabid}",
-        verify=True
-    ).json()
-    related_experiments = sample_data["related_experiments_links"]
-    result = []
-    for exp in related_experiments:
-        experiment_data = requests.get(
-            headers = header,
-            url = f"https://elabftw.fisica.unina.it/api/v2/experiments/{exp.get("entityid")}",
-            verify=True
-        ).json()
-        extra = experiment_data["metadata_decoded"]["extra_fields"]
-        result.append(
-            {"title": exp.get("title"),
-             "layer_number": extra.get("Layer Progressive Number").get("value"),
-             "category": exp.get("category_title"),
-             "deposition_time": extra.get("Duration").get("value"),
-             "repetition_rate": extra.get("Repetition rate").get("value")}
-        )
-    return result
-
-if __name__=="__main__":
-    print("Warning: you're not supposed to be running this as the main program.")

src/main.py

@@ -1,4 +1,5 @@
 import os, json, requests, h5py
+import numpy as np
 from getpass import getpass
 from APIHandler import APIHandler
 from classes import *
@@ -301,7 +302,7 @@ def make_nexus_schema_dictionary(substrate_object, layers):
         }
     return pld_fabrication
 
-def build_nexus_file(pld_fabrication, output_path):
+def build_nexus_file(pld_fabrication, output_path, rheed_osc=None):
     # NOTE: look at the mail attachment from Emiliano...
     with h5py.File(output_path, "w") as f:
         nx_pld_entry = f.create_group("pld_fabrication")
@@ -439,6 +440,9 @@ def build_nexus_file(pld_fabrication, output_path):
             nx_instruments.create_dataset("rheed_system", data = instruments_dict["rheed_system"])
         except TypeError as te:
             raise TypeError(te)
+        nx_rheed = nx_pld_entry.create_group("rheed_data")
+        nx_rheed.attrs["NX_class"] = "NXdata"
+        nx_rheed.create_dataset("intensity", data=rheed_osc)
     return
 
 if __name__=="__main__":
@@ -455,4 +459,6 @@ if __name__=="__main__":
     # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
     with open (f"output/sample-{sample_name}.json", "w") as f:
         json.dump(result, f, indent=3)
-    build_nexus_file(result, output_path=f"output/sample-{sample_name}-nexus.h5")
+    with open(f"tests/Realtime_Window_Analysis.txt", "r") as o:
+        osc = np.loadtxt(o)
+    build_nexus_file(result, output_path=f"output/sample-{sample_name}-nexus.h5", rheed_osc=osc)