PioApocalypse
1b1834d4e6
Target.description defaults to "" (empty str) Substrate.thickness defaults to "" (empty str) Substrate.thickness_unit is now hardcoded to "μm" did you know? apparently h5py does NOT like null values
205 lines
12 KiB
Python
205 lines
12 KiB
Python
import os, json, requests
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from APIHandler import APIHandler
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class Layer:
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'''
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Layer(layer_data) - where layer_data is a Python dictionary.
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Meant to be used for eLabFTW Experiments of the "PLD Deposition" category.
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eLabFTW experiments contain most of the data required by the NeXus file - although every layer is on a different eLab entry;
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unfortunately, some data like the target's chemical formula must be retrieved through additional HTTP requests.
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Attributes 'target_elabid', 'rheed_system_elabid' and 'laser_system_elabid' contain elabid's for these resources, which are all items.
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'''
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def __init__(self, layer_data):
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try:
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self.operator = layer_data["fullname"]
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self.extra = layer_data["metadata_decoded"]["extra_fields"]
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self.layer_number = self.extra["Layer Progressive Number"]["value"] # integer
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self.target_elabid = self.extra["Target"]["value"] # elabid
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self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid
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self.chamber_elabid = self.extra["Chamber"]["value"] # elabid
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self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid
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self.deposition_time = self.extra["Duration"]["value"]
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self.deposition_time_unit = self.extra["Duration"]["unit"]
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self.repetition_rate = self.extra["Repetition rate"]["value"]
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self.repetition_rate_unit = self.extra["Repetition rate"]["unit"]
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try:
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self.number_of_pulses = (float(self.deposition_time) * float(self.repetition_rate)).__floor__()
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except ValueError:
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# Since number_of_pulses is required, if it can't be calculated raise error:
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raise ValueError("""
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Fatal: either Duration or Repetition Rate are empty or invalid.
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This has to be an error, since these fields are required by the NeXus standard.
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Please edit your eLabFTW entry and retry.
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""")
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self.temperature = self.extra["Heater temperature"]["value"] # Note: this field used to have a trailing space in its name
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self.temperature_unit = self.extra["Heater temperature"]["unit"]
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self.process_pressure = self.extra["Process pressure"]["value"] # Note: this field used to have a trailing space in its name
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self.process_pressure_unit = self.extra["Process pressure"]["unit"]
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self.heating_method = self.extra["Heating Method"]["value"]
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self.layer_thickness = self.extra["Thickness"]["value"]
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self.layer_thickness_unit = self.extra["Thickness"]["unit"]
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self.buffer_gas = self.extra["Buffer gas"]["value"]
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self.heater_target_distance = self.extra["Heater-target distance"]["value"]
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self.heater_target_distance_unit = self.extra["Heater-target distance"]["unit"]
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self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity
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self.laser_fluence_unit = "J/(s cm^2)"
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self.laser_spot_area = self.extra["Spot Area"]["value"]
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self.laser_spot_area_unit = "mm^2"
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try:
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self.laser_energy = ( float(self.laser_fluence) * float(self.laser_spot_area) / 100 ).__round__(3)
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self.laser_energy_unit = "J/s"
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except ValueError:
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# Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution:
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print("""
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Warning: either Laser Intensity or Spot Area are empty or invalid.
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If you think this is an error, please edit your eLabFTW entry and retry.
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Setting Laser Energy to NoneType.
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""")
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# Placeholder
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self.laser_energy = None
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# Laser rasternig section
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self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"]["value"]
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self.laser_rastering_positions = self.extra["Laser Rastering Position"]["value"]
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self.laser_rastering_velocities = self.extra["Laser Rastering Speed"]["value"]
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# Pre annealing section
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self.pre_annealing_ambient_gas = self.extra["Buffer gas Pre"]["value"]
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self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"]
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self.pre_annealing_temperature = self.extra["Heater temperature Pre"]["value"]
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self.pre_annealing_duration = self.extra["Duration Pre"]["value"]
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self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"]["unit"]
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self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"]["unit"]
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self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"]
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# Post annealing section
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self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"]
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self.post_annealing_pressure = self.extra["Process pressure PA"]["value"]
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self.post_annealing_temperature = self.extra["Heater temperature PA"]["value"]
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self.post_annealing_duration = self.extra["Duration PA"]["value"]
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self.post_annealing_pressure_unit = self.extra["Process pressure PA"]["unit"]
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self.post_annealing_temperature_unit = self.extra["Heater temperature PA"]["unit"]
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self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"]
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# Rejected but suggested by the NeXus standard:
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#self.laser_rastering_coefficients = None
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except KeyError as k:
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# Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
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# Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
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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.")
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# Optional
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self.start_time = layer_data.get("created_at") or None
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self.description = layer_data.get("body") or None
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def get_instruments(self, apikey):
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raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(self.laser_system_elabid, entryType="items")
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raw_chamber_data = APIHandler(apikey).get_entry_from_elabid(self.chamber_elabid, entryType="items")
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raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid(self.rheed_system_elabid, entryType="items")
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instruments_used = {
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"laser_system": raw_lasersys_data.get("title") or None,
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"deposition_chamber": raw_chamber_data.get("title") or None,
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"rheed_system": raw_rheedsys_data.get("title") or None,
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}
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return instruments_used
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class Entrypoint:
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'''
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Entrypoint(sample_data) - where sample_data is a Python dictionary.
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Meant to be used for eLabFTW Resources of the "Sample" category.
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The entrypoint is the starting point of the process of resolving the data chain.
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The entrypoint must be a dictionary containing the data of a sample, created directly from the JSON of the item endpoint on eLabFTW - which can be done through the function get_entry_from_elabid.
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'''
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def __init__(self, sample_data):
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try:
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self.extra = sample_data["metadata_decoded"]["extra_fields"]
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self.linked_items = sample_data["items_links"] # dict
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self.batch_elabid = self.extra["Substrate batch"]["value"] # elabid
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self.linked_experiments = sample_data["related_experiments_links"] # dict
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self.linked_experiments_elabid = [ i["entityid"] for i in self.linked_experiments ] # list of elabid
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except KeyError as k:
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# Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
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# Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
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raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the sample entry on eLabFTW and make sure you used the correct Resource template.")
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# Non-required attributes:
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self.name = sample_data.get("title") or None # error prevention is more important than preventing empty fields here
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class Material:
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'''
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Material(material_data) - where material_data is a Python dictionary.
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Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories.
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Both a PLD Target and a Substrate are materials made of a certain compound, of which we want to know:
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* Name and formula;
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* Shape and dimensions;
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* Misc.
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'''
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def __init__(self, material_data):
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try:
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self.name = material_data["title"] # required
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self.extra = material_data["metadata_decoded"]["extra_fields"]
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self.compound_elabid = self.extra["Compound"]["value"]
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self.dimensions = str(self.extra["Size"]["value"]) # strings have a .count() method
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if self.dimensions.count("mm") == 2:
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self.dimensions_unit = "mm x mm"
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elif self.dimensions[-1] == '"':
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self.dimensions_unit = "inches"
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else:
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self.dimensions_unit = None
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except KeyError as k:
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# Some keys are not required and can be called through the .get() method - which is permissive and allows null values;
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# Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program:
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raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the target/substrate entry on eLabFTW and make sure you used the correct Resource template.")
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def get_compound_data(self, apikey):
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raw_compound_data = APIHandler(apikey).get_entry_from_elabid(self.compound_elabid, entryType="items")
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name = raw_compound_data["title"]
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extra = raw_compound_data["metadata_decoded"]["extra_fields"]
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formula = extra.get("Chemical formula")
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cas = extra.get("CAS number ") or { "value": None }
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compound_data = {
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"name" : name,
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"chemical_formula" : formula.get("value"),
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"cas_number" : cas.get("value")
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}
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return compound_data
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def get_compound_formula(self, apikey):
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formula = self.get_compound_data(apikey).get("chemical_formula")
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return formula
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class Substrate(Material):
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def __init__(self, material_data):
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super().__init__(material_data)
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try:
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self.orientation = self.extra["Orientation"]["value"]
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self.miscut_angle = self.extra["Miscut Angle"]["value"]
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self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"]
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self.miscut_direction = self.extra["Miscut Direction"]["value"]
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# Not present (yet) on eLabFTW for Substrates:
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self.thickness = "" #self.extra["Thickness"]["value"]
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self.thickness_unit = "μm" #self.extra["Thickness"]["unit"]
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self.surface_treatment = self.extra["Surface treatment"]["value"]
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self.manufacturer = self.extra["Supplier"]["value"]
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self.batch_id = self.extra["Batch ID"]["value"]
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except KeyError as k:
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raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for substrates. Check the {self.name} substrate entry on eLabFTW and make sure you used the correct Resource template.")
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class Target(Material):
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def __init__(self, material_data):
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super().__init__(material_data)
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try:
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self.thickness = self.extra["Thickness"]["value"]
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self.thickness_unit = self.extra["Thickness"]["unit"]
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self.shape = self.extra["shape"]["value"]
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self.solid_form = self.extra["Solid form"]["value"]
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self.manufacturer = self.extra["Supplier"]["value"]
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except KeyError as k:
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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.")
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# Non-required attributes:
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self.description = material_data.get("body") or ""
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if __name__=="__main__":
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head = Header("MyApiKey-123456789abcdef")
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print(f"Example header:\n\t{head.header}\n")
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print("Warning: you're not supposed to be running this as the main program.") |