removes debug line, writes json to file instead (path: output/)

only lacks units of measurement, then I'll be ready for conversion

.gitignore

@@ -1,6 +1,9 @@
-# ignora log di h5tojson e jsontoh5
+# ignores logs of h5tojson, jsontoh5
 *.log
 
+# ignores output json of main.py
+output/*.json
+
 # ---> Python
 # Byte-compiled / optimized / DLL files
 __pycache__/

src/classes.py

@@ -16,8 +16,9 @@ class Layer:
             self.extra = layer_data["metadata_decoded"]["extra_fields"]
             self.layer_number = self.extra["Layer Progressive Number"]["value"] # integer
             self.target_elabid = self.extra["Target"]["value"] # elabid
-            self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid
             self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid
+            self.chamber_elabid = self.extra["Chamber"]["value"] # elabid
+            self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid
             self.start_time = layer_data.get("created_at")
             self.operator = layer_data.get("fullname")
             self.description = layer_data.get("body")
@@ -71,6 +72,16 @@ class Layer:
             # Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
             # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
             raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the deposition layer entry on eLabFTW and make sure you used the correct Experiment template.")
+    def get_instruments(self, apikey):
+        raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(self.laser_system_elabid, entryType="items")
+        raw_chamber_data = APIHandler(apikey).get_entry_from_elabid(self.chamber_elabid, entryType="items")
+        raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid(self.rheed_system_elabid, entryType="items")
+        instruments_used = {
+            "laser_system": raw_lasersys_data.get("title") or None,
+            "deposition_chamber": raw_chamber_data.get("title") or None,
+            "rheed_system": raw_rheedsys_data.get("title") or None,
+        }
+        return instruments_used
 
 class Entrypoint:
     '''

src/main.py

@@ -98,7 +98,37 @@ def chain_layer_to_target(layer_object):
     material_object = call_material_from_elabid(target_elabid)
     return material_object
 
+def deduplicate_instruments_from_layers(layers):
+    '''
+    Takes a list of Layer-class objects and for each layer gets the instruments used (laser, depo chamber and RHEED), returns deduplicated list. Ideally, the lists should only contain one element.
+    '''
+    lasers = []
+    chambers = []
+    rheeds = []
+    for lyr in layers:
+        instruments = lyr.get_instruments(apikey)
+        lasers.append(instruments["laser_system"])
+        chambers.append(instruments["deposition_chamber"])
+        rheeds.append(instruments["rheed_system"])
+    instruments_used_dict = {
+        "laser_system": list( set( lasers ) ),
+        "deposition_chamber": list( set( chambers ) ),
+        "rheed_system" : list( set( rheeds ) ),
+    }
+    # lasers = { f"layer_{lyr.layer_number}": lyr.laser_system for lyr in layers }
+    # chambers = { f"layer_{lyr.layer_number}": lyr.deposition_chamber for lyr in layers }
+    # rheeds = { f"layer_{lyr.layer_number}": lyr.rheed_system for lyr in layers }
+    # instruments_used_dict = {
+    #     "laser_system": lasers,
+    #     "deposition_chamber": chambers,
+    #     "rheed_system": rheeds,
+    # }
+    return instruments_used_dict
+
 def make_nexus_schema_dictionary(substrate_object, layers):
+    '''
+    Main function, takes all the other functions to reconstruct the full dataset. Takes a Substrate-class object (output of the chain_entrypoint_to_batch() function) and a list of Layer-class objects (output of the chain_entrypoint_to_layers() function), returns dictionary with the same schema as the NeXus standard for PLD fabrications.
+    '''
     pld_fabrication = {
         "sample": {
             "substrate": {
@@ -115,6 +145,7 @@ def make_nexus_schema_dictionary(substrate_object, layers):
             },
             "multilayer": {},
         },
+        "instruments_used": deduplicate_instruments_from_layers(layers),
     }
     multilayer = pld_fabrication["sample"]["multilayer"]
     for layer in layers:
@@ -133,9 +164,41 @@ def make_nexus_schema_dictionary(substrate_object, layers):
             # "batch_id" : target_object.batch_id,
         }
         multilayer[name] = {
-            "target": target_dict
+            "target": target_dict,
+            "start_time": layer.start_time,
+            "operator": layer.operator,
+            "description": layer.description,
+            "number_of_pulses": layer.number_of_pulses,
+            "deposition_time": layer.deposition_time,
+            "temperature": layer.temperature,
+            "heating_method": layer.heating_method,
+            "layer_thickness": layer.layer_thickness,
+            "buffer_gas": layer.buffer_gas,
+            "process_pressure": layer.process_pressure,
+            "heater_target_distance": layer.heater_target_distance,
+            "repetition_rate": layer.repetition_rate,
+            "laser_fluence": layer.laser_fluence,
+            "laser_spot_area": layer.laser_spot_area,
+            "laser_energy": layer.laser_energy,
+            "laser_rastering": {
+                "geometry": layer.laser_rastering_geometry,
+                "positions": layer.laser_rastering_positions,
+                "velocities": layer.laser_rastering_velocities,
+            },
+            "pre_annealing": {
+                "ambient_gas": layer.pre_annealing_ambient_gas,
+                "pressure": layer.pre_annealing_pressure,
+                "temperature": layer.pre_annealing_temperature,
+                "duration": layer.pre_annealing_duration,
+            },
+            "post_annealing": {
+                "ambient_gas": layer.post_annealing_ambient_gas,
+                "pressure": layer.post_annealing_pressure,
+                "temperature": layer.post_annealing_temperature,
+                "duration": layer.post_annealing_duration,
+            },
         }
-    return json.dumps(pld_fabrication, indent=2)
+    return pld_fabrication
 
 if __name__=="__main__":
     # TO-DO: place the API base URL somewhere else. 
@@ -146,4 +209,7 @@ if __name__=="__main__":
     sample = Entrypoint(data)
     substrate_object = chain_entrypoint_to_batch(sample) # Substrate-class object
     layers = chain_entrypoint_to_layers(sample) # list of Layer-class objects
-    print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
+    result = make_nexus_schema_dictionary(substrate_object, layers)
+    # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
+    with open (f"output/sample-{elabid}.json", "w") as f:
+        json.dump(result, f, indent=3)