more elegant solution for deduplicating instruments

also edits help for deduplicate_instruments... to better explain what it
does; also fixes small typo ('default=' instead of 'default ='), row 448

.gitignore

@@ -1,6 +1,11 @@
-# ignora log di h5tojson e jsontoh5
+# ignores logs of h5tojson, jsontoh5
 *.log
 
+# ignores any output of main.py
+output/*.json
+output/*.h5
+output/*.nxs
+
 # ---> Python
 # Byte-compiled / optimized / DLL files
 __pycache__/

requirements.txt

@@ -1,2 +1,3 @@
 requests
 asyncio
+h5py

src/APIHandler.py

@@ -33,6 +33,8 @@ class APIHandler:
                     raise ConnectionError(f"Invalid API key or authentication method.")
                 case 404:
                     raise ConnectionError(f"404: Not Found. This means there's no resource with this elabid (wrong elabid?) on your eLabFTW (wrong endpoint?).")
+                case 400:
+                    raise ConnectionError(f"400: Bad Request. This means the API endpoint you tried to reach is invalid. Did you tamper with the source code? If not, contact the developer.")
                 case _:
                     raise ConnectionError(f"HTTP request failed with status code: {response.status_code} (NOTE: 4xx means user's fault).")
         else:

src/classes.py

@@ -13,16 +13,17 @@ class Layer:
     '''
     def __init__(self, layer_data):
         try:
+            self.operator = layer_data["fullname"]
             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.start_time = layer_data.get("created_at")
+            self.chamber_elabid = self.extra["Chamber"]["value"] # elabid
-            self.operator = layer_data.get("fullname")
+            self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid
-            self.description = layer_data.get("body")
             self.deposition_time = self.extra["Duration"]["value"]
+            self.deposition_time_unit = self.extra["Duration"]["unit"]
             self.repetition_rate = self.extra["Repetition rate"]["value"]
+            self.repetition_rate_unit = self.extra["Repetition rate"]["unit"]
             try:
                 self.number_of_pulses = (float(self.deposition_time) * float(self.repetition_rate)).__floor__()
             except ValueError:
@@ -33,15 +34,22 @@ class Layer:
     Please edit your eLabFTW entry and retry.
                 """)
             self.temperature = self.extra["Heater temperature"]["value"] # Note: this field used to have a trailing space in its name
+            self.temperature_unit = self.extra["Heater temperature"]["unit"]
             self.process_pressure = self.extra["Process pressure"]["value"] # Note: this field used to have a trailing space in its name
+            self.process_pressure_unit = self.extra["Process pressure"]["unit"]
             self.heating_method = self.extra["Heating Method"]["value"]
             self.layer_thickness = self.extra["Thickness"]["value"]
+            self.layer_thickness_unit = self.extra["Thickness"]["unit"]
             self.buffer_gas = self.extra["Buffer gas"]["value"]
             self.heater_target_distance = self.extra["Heater-target distance"]["value"]
+            self.heater_target_distance_unit = self.extra["Heater-target distance"]["unit"]
             self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity
+            self.laser_fluence_unit = "J/(s cm^2)"
             self.laser_spot_area = self.extra["Spot Area"]["value"]
+            self.laser_spot_area_unit = "mm^2"
             try:
-                self.laser_energy = (float(self.laser_fluence) * float(self.laser_spot_area)).__round__(3)
+                self.laser_energy = ( float(self.laser_fluence) * float(self.laser_spot_area) / 100 ).__round__(3)
+                self.laser_energy_unit = "J/s"
             except ValueError:
                 # Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution:
                 print("""
@@ -60,17 +68,37 @@ class Layer:
             self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"]
             self.pre_annealing_temperature = self.extra["Heater temperature Pre"]["value"]
             self.pre_annealing_duration = self.extra["Duration Pre"]["value"]
+            self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"]["unit"]
+            self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"]["unit"]
+            self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"]
             # Post annealing section
             self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"]
             self.post_annealing_pressure = self.extra["Process pressure PA"]["value"]
             self.post_annealing_temperature = self.extra["Heater temperature PA"]["value"]
             self.post_annealing_duration = self.extra["Duration PA"]["value"]
+            self.post_annealing_pressure_unit = self.extra["Process pressure PA"]["unit"]
+            self.post_annealing_temperature_unit = self.extra["Heater temperature PA"]["unit"]
+            self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"]
+
             # Rejected but suggested by the NeXus standard:
             #self.laser_rastering_coefficients = None
         except KeyError as k:
             # 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.")
+        # Optional
+        self.start_time = layer_data.get("created_at") or None
+        self.description = layer_data.get("body") or None
+    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:
     '''
@@ -111,7 +139,13 @@ class Material:
             self.name = material_data["title"] # required
             self.extra = material_data["metadata_decoded"]["extra_fields"]
             self.compound_elabid = self.extra["Compound"]["value"]
-            self.dimensions = self.extra["Size"]["value"]
+            self.dimensions = str(self.extra["Size"]["value"]) # strings have a .count() method
+            if self.dimensions.count("mm") == 2:
+                self.dimensions_unit = "mm x mm"
+            elif self.dimensions[-1] == '"':
+                self.dimensions_unit = "inches"
+            else:
+                self.dimensions_unit = None
         except KeyError as k:
             # 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:
@@ -138,9 +172,11 @@ class Substrate(Material):
         try:
             self.orientation = self.extra["Orientation"]["value"]
             self.miscut_angle = self.extra["Miscut Angle"]["value"]
+            self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"]
             self.miscut_direction = self.extra["Miscut Direction"]["value"]
             # Not present (yet) on eLabFTW for Substrates:
-            self.thickness = None #self.extra["Thickness"]["value"]
+            self.thickness = "" #self.extra["Thickness"]["value"]
+            self.thickness_unit = "μm" #self.extra["Thickness"]["unit"]
             self.surface_treatment = self.extra["Surface treatment"]["value"]
             self.manufacturer = self.extra["Supplier"]["value"]
             self.batch_id = self.extra["Batch ID"]["value"]
@@ -152,11 +188,14 @@ class Target(Material):
         super().__init__(material_data)
         try:
             self.thickness = self.extra["Thickness"]["value"]
+            self.thickness_unit = self.extra["Thickness"]["unit"]
             self.shape = self.extra["shape"]["value"]
             self.solid_form = self.extra["Solid form"]["value"]
             self.manufacturer = self.extra["Supplier"]["value"]
         except KeyError as k:
             raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for PLD targets. Check the {self.name} target entry on eLabFTW and make sure you used the correct Resource template.")
+        # Non-required attributes:
+        self.description = material_data.get("body") or ""
 
 
 

src/main.py

@@ -1,4 +1,4 @@
-import os, json, requests
+import os, json, requests, h5py
 from getpass import getpass
 from APIHandler import APIHandler
 from classes import *
@@ -98,71 +98,361 @@ def chain_layer_to_target(layer_object):
     material_object = call_material_from_elabid(target_elabid)
     return material_object
 
-#sample_object = call_entrypoint_from_elabid(elabid)
+def deduplicate_instruments_from_layers(layers):
-#from_entrypoint_to_material(sample_object)
+    '''
+    Takes a list of Layer-class objects and for each layer gets the instruments used (laser, depo chamber and RHEED), returns dictionary with one item per category. This means that if more layers share the same instruments it returns a dictionary with just their names as strings (no lists or sub-dictionaries).
     
+    If different layers have different instruments (e.g. laser systems) the user is prompted to only select one.
+    '''
+    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"])
+    ded_lasers = list( set( lasers ) )
+    ded_chambers = list( set( chambers ) )
+    ded_rheeds = list( set( rheeds ) )
+    elegant_dict = {
+        # Keep key names human readable since they're used in the messages of the following errors
+        "Laser Systems": ded_lasers,
+        "Deposition Chamber": ded_chambers,
+        "RHEED Systems": ded_rheeds
+    } # dictionary's name's a joke
+    updated_dict = {} # use this for containing the final dataset
+    for ded in elegant_dict:
+        if len(elegant_dict[ded]) == 0:
+            # if len of list is 0 - empty list - raise error
+            raise IndexError(f"Missing data: no Laser System, Chamber and/or RHEED System is specified in any of the Deposition-type experiments related to this sample. Fix this on eLabFTW before retrying. Affected list: {ded}.")
+        elif len(elegant_dict[ded]) > 1:
+            # if len of list is > 1 - too many values - allow the user to pick one
+            print("Warning: different instruments have been used for different layers - which is currently not allowed.")
+            # there's a better way to do this but I can't remember now for the life of me...
+            i = 0
+            while i < len(elegant_dict[ded]):
+                print(f"{i} - {elegant_dict[ded][i]}")
+                i += 1
+            ans = None
+            while not type(ans) == int or not ans in range(0, len(elegant_dict[ded])):
+                ans = input("Please pick one of the previous (0, 1, ...) [default = 0]: ") or "0"
+                if ans.isdigit():
+                    ans = int(ans)
+                continue # unnecessary?
+            updated_dict[ded] = elegant_dict[ded][ans]
+        elif elegant_dict[ded][0] in ["", 0, None]:
+            # if len is 1 BUT value is "", 0 or None raise error
+            raise ValueError(f"Missing data: a Laser System, Chamber and/or RHEED System which is specified across all the Deposition-type experiments related to this sample is either empty or invalid. Fix this on eLabFTW before retrying. Affected list: {ded}.")
+        else:
+            # if none of the previous (only 1 value), that single value is used
+            updated_dict[ded] = elegant_dict[ded][0]
+    instruments_used_dict = {
+        "laser_system": updated_dict["Laser Systems"],
+        "deposition_chamber": updated_dict["Deposition Chamber"],
+        "rheed_system": updated_dict["RHEED Systems"],
+    }
+    return instruments_used_dict
+    
+    ### OLD CODE
+    # if 0 in [ len(i) for i in elegant_list ]:
+    #     # i.e. if length of one of the lists in elegant_list is zero (missing data):
+    #     raise IndexError("Missing data: no Laser System, Chamber and/or RHEED System is specified in any of the Deposition-type experiments related to this sample.")
+    # if not all([ len(i) == 1 for i in elegant_list ]):
+    #     print("Warning: different instruments have been used for different layers - which is currently not allowed.")
+    #     # for every element in elegant list check if len > 1 and if it is 
+    #     print("Selecting the first occurence for every category...")
+    ###
+    # 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,
+    # }
+
+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": {
+                "name": substrate_object.name,
+                "chemical_formula" : substrate_object.get_compound_formula(apikey),
+                "orientation" : substrate_object.orientation,
+                "miscut_angle" : {
+                    "value": substrate_object.miscut_angle,
+                    "units": substrate_object.miscut_angle_unit
+                },
+                "miscut_direction" : substrate_object.miscut_direction,
+                "thickness" : {
+                    "value": substrate_object.thickness,
+                    "units": substrate_object.thickness_unit,
+                },
+                "dimensions" : substrate_object.dimensions,
+                "surface_treatment" : substrate_object.surface_treatment,
+                "manufacturer" : substrate_object.manufacturer,
+                "batch_id" : substrate_object.batch_id,
+            },
+            "multilayer": {},
+        },
+        "instruments_used": deduplicate_instruments_from_layers(layers),
+    }
+    multilayer = pld_fabrication["sample"]["multilayer"]
+    for layer in layers:
+        name = "layer_" + layer.layer_number
+        target_object = chain_layer_to_target(layer)
+        target_dict = {
+            "name": target_object.name,
+            "chemical_formula" : target_object.get_compound_formula(apikey),
+            "description" : target_object.description,
+            "shape" : target_object.shape,
+            "dimensions" : target_object.dimensions,
+            "thickness" : {
+                "value": target_object.thickness,
+                "units": target_object.thickness_unit,
+            },
+            "solid_form" : target_object.solid_form,
+            "manufacturer" : target_object.manufacturer,
+            "batch_id" : target_object.name,
+            # TO-DO: currently not available:
+        }
+        multilayer[name] = {
+            "target": target_dict,
+            "start_time": layer.start_time,
+            "operator": layer.operator,
+            "description": layer.description,
+            "number_of_pulses": layer.number_of_pulses,
+            "deposition_time": {
+                "value": layer.deposition_time,
+                "units": layer.deposition_time_unit,
+            },
+            "temperature": {
+                "value": layer.temperature,
+                "units": layer.temperature_unit,
+            },
+            "heating_method": layer.heating_method,
+            "layer_thickness": {
+                "value": layer.layer_thickness,
+                "units": layer.layer_thickness_unit,
+            },
+            "buffer_gas": layer.buffer_gas,
+            "process_pressure": {
+                "value": layer.process_pressure,
+                "units": layer.process_pressure_unit,
+            },
+            "heater_target_distance": {
+                "value": layer.heater_target_distance,
+                "units": layer.heater_target_distance_unit,
+            },
+            "repetition_rate": {
+                "value": layer.repetition_rate,
+                "units": layer.repetition_rate_unit,
+            },
+            "laser_fluence": {
+                "value": layer.laser_fluence,
+                "units": layer.laser_fluence_unit,
+            },
+            "laser_spot_area": {
+                "value": layer.laser_spot_area,
+                "units": layer.laser_spot_area_unit,
+            },
+            "laser_energy": {
+                "value": layer.laser_energy,
+                "units": layer.laser_energy_unit,
+            },
+            "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": {
+                    "value": layer.pre_annealing_pressure,
+                    "units": layer.pre_annealing_pressure_unit,
+                },
+                "temperature": {
+                    "value": layer.pre_annealing_temperature,
+                    "units": layer.pre_annealing_temperature_unit,
+                },
+                "duration": {
+                    "value": layer.pre_annealing_duration,
+                    "units": layer.pre_annealing_duration_unit,
+                },
+            },
+            "post_annealing": {
+                "ambient_gas": layer.post_annealing_ambient_gas,
+                "pressure": {
+                    "value": layer.post_annealing_pressure,
+                    "units": layer.post_annealing_pressure_unit,
+                },
+                "temperature": {
+                    "value": layer.post_annealing_temperature,
+                    "units": layer.post_annealing_temperature_unit,
+                },
+                "duration": {
+                    "value": layer.post_annealing_duration,
+                    "units": layer.post_annealing_duration_unit,
+                },
+            },
+        }
+    return pld_fabrication
+
+def build_nexus_file(pld_fabrication, output_path):
+    # NOTE: look at the mail attachment from Emiliano...
+    with h5py.File(output_path, "w") as f:
+        nx_pld_entry = f.create_group("pld_fabrication")
+        nx_pld_entry.attrs["NX_class"] = "NXentry"
+
+        # Sample section
+        nx_sample = nx_pld_entry.create_group("sample")
+        nx_sample.attrs["NX_class"] = "NXsample"
+        sample_dict = pld_fabrication["sample"]
+
+        # Substrate sub-section
+        nx_substrate = nx_sample.create_group("substrate")
+        nx_substrate.attrs["NX_class"] = "NXsubentry"
+        substrate_dict = sample_dict["substrate"]
+        try:
+            # Substrate fields (datasets)
+            nx_substrate.create_dataset("name", data=substrate_dict["name"])
+            nx_substrate.create_dataset("chemical_formula", data=substrate_dict["chemical_formula"])
+            nx_substrate.create_dataset("orientation", data=substrate_dict["orientation"])
+            nx_substrate.create_dataset("miscut_angle", data=substrate_dict["miscut_angle"]["value"]) # float
+            nx_substrate["miscut_angle"].attrs["units"] = substrate_dict["miscut_angle"]["units"]
+            nx_substrate.create_dataset("miscut_direction", data=substrate_dict["miscut_direction"])
+            nx_substrate.create_dataset("thickness", data=substrate_dict["thickness"]["value"]) # float/int
+            nx_substrate["thickness"].attrs["units"] = substrate_dict["thickness"]["units"]
+            nx_substrate.create_dataset("dimensions", data=substrate_dict["dimensions"])
+            nx_substrate.create_dataset("surface_treatment", data=substrate_dict["surface_treatment"])
+            nx_substrate.create_dataset("manufacturer", data=substrate_dict["manufacturer"])
+            nx_substrate.create_dataset("batch_id", data=substrate_dict["batch_id"])
+        except TypeError as te:
+            # sooner or later I'll handle this too - not today tho
+            raise TypeError(te)
+
+        # Multilayer sub-section
+        nx_multilayer = nx_sample.create_group("multilayer")
+        nx_multilayer.attrs["NX_class"] = "NXsubentry"
+        multilayer_dict = sample_dict["multilayer"]
+        # Repeat FOR EACH LAYER:
+        for layer in multilayer_dict:
+            nx_layer = nx_multilayer.create_group(layer)
+            nx_layer.attrs["NX_class"] = "NXsubentry"
+            layer_dict = multilayer_dict[layer]
+            # Sub-groups of a layer
+            ## Target
+            nx_target = nx_layer.create_group("target")
+            nx_target.attrs["NX_class"] = "NXsample"
+            target_dict = layer_dict["target"]
+            ## Rastering and Annealing
+            nx_laser_rastering = nx_layer.create_group("laser_rastering")
+            nx_laser_rastering.attrs["NX_class"] = "NXprocess"
+            rastering_dict = layer_dict["laser_rastering"]
+            nx_pre_annealing = nx_layer.create_group("pre_annealing")
+            nx_pre_annealing.attrs["NX_class"] = "NXprocess"
+            pre_ann_dict = layer_dict["pre_annealing"]
+            nx_post_annealing = nx_layer.create_group("post_annealing")
+            nx_post_annealing.attrs["NX_class"] = "NXprocess"
+            post_ann_dict = layer_dict["post_annealing"]
+
+            ## Target metadata
+            try:
+                nx_target.create_dataset("name", data = target_dict["name"])
+                nx_target.create_dataset("chemical_formula", data = target_dict["chemical_formula"])
+                nx_target.create_dataset("description", data = target_dict["description"])
+                nx_target.create_dataset("shape", data = target_dict["shape"])
+                nx_target.create_dataset("dimensions", data = target_dict["dimensions"])
+                nx_target.create_dataset("thickness", data = target_dict["thickness"]["value"]) # float/int
+                nx_target["thickness"].attrs["units"] = target_dict["thickness"]["units"]
+                nx_target.create_dataset("solid_form", data = target_dict["solid_form"])
+                nx_target.create_dataset("manufacturer", data = target_dict["manufacturer"])
+                nx_target.create_dataset("batch_id", data = target_dict["batch_id"])
+            except TypeError as te:
+                raise TypeError(te)
+            ## Other layer-specific metadata
+            try:
+                nx_layer.create_dataset("start_time", data = layer_dict["start_time"])
+                nx_layer.create_dataset("operator", data = layer_dict["operator"])
+                nx_layer.create_dataset("number_of_pulses", data = layer_dict["number_of_pulses"])
+                nx_layer.create_dataset("deposition_time", data = layer_dict["deposition_time"]["value"])
+                nx_layer["deposition_time"].attrs["units"] = layer_dict["deposition_time"]["units"]
+                nx_layer.create_dataset("repetition_rate", data = layer_dict["repetition_rate"]["value"])
+                nx_layer["repetition_rate"].attrs["units"] = layer_dict["repetition_rate"]["units"]
+                nx_layer.create_dataset("temperature", data = layer_dict["temperature"]["value"])
+                nx_layer["temperature"].attrs["units"] = layer_dict["temperature"]["units"]
+                nx_layer.create_dataset("heating_method", data = layer_dict["heating_method"])
+                nx_layer.create_dataset("layer_thickness", data = layer_dict["layer_thickness"]["value"])
+                nx_layer["layer_thickness"].attrs["units"] = layer_dict["layer_thickness"]["units"]
+                nx_layer.create_dataset("buffer_gas", data = layer_dict["buffer_gas"])
+                nx_layer.create_dataset("process_pressure", data = layer_dict["process_pressure"]["value"])
+                nx_layer["process_pressure"].attrs["units"] = layer_dict["process_pressure"]["units"]
+                nx_layer.create_dataset("heater_target_distance", data = layer_dict["heater_target_distance"]["value"])
+                nx_layer["heater_target_distance"].attrs["units"] = layer_dict["heater_target_distance"]["units"]
+                nx_layer.create_dataset("laser_fluence", data = layer_dict["laser_fluence"]["value"])
+                nx_layer["laser_fluence"].attrs["units"] = layer_dict["laser_fluence"]["units"]
+                nx_layer.create_dataset("laser_spot_area", data = layer_dict["laser_spot_area"]["value"])
+                nx_layer["laser_spot_area"].attrs["units"] = layer_dict["laser_spot_area"]["units"]
+                nx_layer.create_dataset("laser_energy", data = layer_dict["laser_energy"]["value"])
+                nx_layer["laser_energy"].attrs["units"] = layer_dict["laser_energy"]["units"]
+            except TypeError as te:
+                raise TypeError(te)
+            ## Rastering metadata
+            try:
+                nx_laser_rastering.create_dataset("geometry", data = rastering_dict["geometry"])
+                nx_laser_rastering.create_dataset("positions", data = rastering_dict["positions"])
+                nx_laser_rastering.create_dataset("velocities", data = rastering_dict["velocities"])
+            except TypeError as te:
+                raise TypeError(te)
+            ## Annealing metadata
+            try:
+                nx_pre_annealing.create_dataset("ambient_gas", data = pre_ann_dict["ambient_gas"])
+                nx_pre_annealing.create_dataset("pressure", data = pre_ann_dict["pressure"]["value"])
+                nx_pre_annealing["pressure"].attrs["units"] = pre_ann_dict["pressure"]["units"]
+                nx_pre_annealing.create_dataset("temperature", data = pre_ann_dict["temperature"]["value"])
+                nx_pre_annealing["temperature"].attrs["units"] = pre_ann_dict["temperature"]["units"]
+                nx_pre_annealing.create_dataset("duration", data = pre_ann_dict["duration"]["value"])
+                nx_pre_annealing["duration"].attrs["units"] = pre_ann_dict["duration"]["units"]
+            except TypeError as te:
+                raise TypeError(te)
+            try:
+                nx_post_annealing.create_dataset("ambient_gas", data = post_ann_dict["ambient_gas"])
+                nx_post_annealing.create_dataset("pressure", data = post_ann_dict["pressure"]["value"])
+                nx_post_annealing["pressure"].attrs["units"] = post_ann_dict["pressure"]["units"]
+                nx_post_annealing.create_dataset("temperature", data = post_ann_dict["temperature"]["value"])
+                nx_post_annealing["temperature"].attrs["units"] = post_ann_dict["temperature"]["units"]
+                nx_post_annealing.create_dataset("duration", data = post_ann_dict["duration"]["value"])
+                nx_post_annealing["duration"].attrs["units"] = post_ann_dict["duration"]["units"]
+            except TypeError as te:
+                raise TypeError(te)
+        
+        # Instruments used section
+        nx_instruments = nx_pld_entry.create_group("instruments_used")
+        nx_instruments.attrs["NX_class"] = "NXinstrument"
+        instruments_dict = pld_fabrication["instruments_used"]
+        try:
+            nx_instruments.create_dataset("laser_system", data = instruments_dict["laser_system"])
+            nx_instruments.create_dataset("deposition_chamber", data = instruments_dict["deposition_chamber"])
+            nx_instruments.create_dataset("rheed_system", data = instruments_dict["rheed_system"])
+        except TypeError as te:
+            raise TypeError(te)
+    return
 
 if __name__=="__main__":
-    print(f"=======================\n===== DEBUG MODE! =====\n=======================\n")
+    # TO-DO: place the API base URL somewhere else. 
     ELABFTW_API_URL = "https://elabftw.fisica.unina.it/api/v2"
     apikey = getpass("Paste API key here: ")
-    elabid = input("Enter elabid of your starting sample [default= 1111]: ") or 1111
+    elabid = input("Enter elabid of your starting sample [default = 1111]: ") or 1111
     data = APIHandler(apikey).get_entry_from_elabid(elabid)
     sample = Entrypoint(data)
-    batch = chain_entrypoint_to_batch(sample) # Material-class object
+    sample_name = sample.name.strip().replace(" ","_")
-    bd = batch.__dict__
+    substrate_object = chain_entrypoint_to_batch(sample) # Substrate-class object
-    bd.pop("extra")
     layers = chain_entrypoint_to_layers(sample) # list of Layer-class objects
-    print(f"Sample name:\n{sample.name}\n")
+    result = make_nexus_schema_dictionary(substrate_object, layers)
-    print(f"Substrate data:\n{bd}\n")
+    # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
-    print(f"Layers data:")
+    with open (f"output/sample-{sample_name}.json", "w") as f:
-    for layer in layers:
+        json.dump(result, f, indent=3)
-        ld = layer.__dict__
+    build_nexus_file(result, output_path=f"output/sample-{sample_name}-nexus.h5")
-        ld.pop("extra")
-        tgt = chain_layer_to_target(layer)
-        td = tgt.__dict__
-        td.pop("extra")
-        print(ld)
-        print(td)
-        print()
-
-    # entryType = None
-    # while entryType not in ["items", "experiments"]:
-    #     eT = input("Enter a valid entry type [items, experiments]: ")
-    #     # This allows for a shortcut: instead of prompting the type before and the elabid after I can just prompt both at the same time - e.g. e51 is exp. 51, i1108 is item 1108...
-    #     if eT[0] in ["e", "i"] and eT[-1].isnumeric():
-    #         try:
-    #             elabid = int(eT[1:])
-    #             eT = eT[0]
-    #         except Exception:
-    #             print("Usage: i|item|items|i[ELABID] for items, e|experiment|experiments|e[ELABID] for experiments.")
-    #             continue
-    #     match eT:
-    #         case "items" | "i" | "item":
-    #             entryType = "items"
-    #         case "experiments" | "e" | "exp" | "experiment":
-    #             entryType = "experiments"
-    #         case _:
-    #             continue
-    # # This will probably be reworked in production
-    # try:
-    #     elabid = elabid
-    # except NameError:
-    #     elabid = input("Input elabid here [default = 1111]: ") or 1111
-    # data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType)
-    # if entryType == "experiments":
-    #     layer = Layer(data)
-    #     result = layer.__dict__
-    #     result.pop("extra")
-    #     print(result)
-    # elif entryType == "items":
-    #     if data.get("category_title") == "Sample":
-    #         item = Entrypoint(data)
-    #     elif data.get("category_title") in ["PLD Target", "Substrate"]:
-    #         item = Material(data)
-    #         print(item.get_compound_formula(apikey))
-    #     else:
-    #         raise Exception("The selected item or experiment is not in one of the following categories: [Sample, PLD Target, Substrate, PLD Deposition].")
-    #     result = item.__dict__
-    #     result.pop("extra")
-    #     print(result)