adds units of measurement (UoM) in Material class and children

plus moves around fullname/operator, created_at and description/body so
that operator is required while the others aren't

requirements.txt

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

src/classes.py

@@ -13,17 +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.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")
             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:
@@ -34,15 +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("""
@@ -61,17 +68,27 @@ 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")
@@ -122,7 +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:
@@ -149,6 +172,7 @@ 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"]
@@ -163,13 +187,14 @@ 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 ""
+        self.description = material_data.get("body") or None
 
 
 

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 *
@@ -200,6 +200,21 @@ def make_nexus_schema_dictionary(substrate_object, layers):
         }
     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"
+
+        # Substrate section
+        nx_substrate = nx_pld_entry.create_group("substrate")
+        nx_substrate.attrs["NX_class"] = "NXsubentry"
+    pass
+
 if __name__=="__main__":
     # TO-DO: place the API base URL somewhere else. 
     ELABFTW_API_URL = "https://elabftw.fisica.unina.it/api/v2"