emanuele/eXParser-PLD
SHA256
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 2 Wiki Activity

LazyVim tab fix + new unused Layer-class methods to fetch uploads

Browse Source
This commit is contained in:
Emanuele D'Amico
2026-05-08 18:09:03 +02:00
parent 51b8ea7dd7
commit 008bcff826
1 changed files with 130 additions and 53 deletions
Download Patch File Download Diff File Expand all files Collapse all files

183
src/classes.py
View File

@@ -1,8 +1,9 @@
import os, json, requests import os, json, requests
from APIHandler import APIHandler from APIHandler import APIHandler
class Layer: class Layer:
''' """
Layer(layer_data) - where layer_data is a Python dictionary. Layer(layer_data) - where layer_data is a Python dictionary.
Meant to be used for eLabFTW Experiments of the "PLD Deposition" category. Meant to be used for eLabFTW Experiments of the "PLD Deposition" category.
@@ -10,22 +11,27 @@ class Layer:
eLabFTW experiments contain most of the data required by the NeXus file - although every layer is on a different eLab entry; eLabFTW experiments contain most of the data required by the NeXus file - although every layer is on a different eLab entry;
unfortunately, some data like the target's chemical formula must be retrieved through additional HTTP requests. unfortunately, some data like the target's chemical formula must be retrieved through additional HTTP requests.
Attributes 'target_elabid', 'rheed_system_elabid' and 'laser_system_elabid' contain elabid's for these resources, which are all items. Attributes 'target_elabid', 'rheed_system_elabid' and 'laser_system_elabid' contain elabid's for these resources, which are all items.
''' """
def __init__(self, layer_data): def __init__(self, layer_data):
try: try:
self.operator = layer_data["fullname"] self.operator = layer_data["fullname"]
self.extra = layer_data["metadata_decoded"]["extra_fields"] self.extra = layer_data["metadata_decoded"]["extra_fields"]
self.layer_number = self.extra["Layer Progressive Number"]["value"] # integer self.layer_number = self.extra["Layer Progressive Number"][
self.target_elabid = self.extra["Target"]["value"] # elabid "value"
self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid ] # integer
self.chamber_elabid = self.extra["Chamber"]["value"] # elabid 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.deposition_time = self.extra["Duration"]["value"] self.deposition_time = self.extra["Duration"]["value"]
self.deposition_time_unit = self.extra["Duration"]["unit"] self.deposition_time_unit = self.extra["Duration"]["unit"]
self.repetition_rate = self.extra["Repetition rate"]["value"] self.repetition_rate = self.extra["Repetition rate"]["value"]
self.repetition_rate_unit = self.extra["Repetition rate"]["unit"] self.repetition_rate_unit = self.extra["Repetition rate"]["unit"]
try: try:
self.number_of_pulses = (float(self.deposition_time) * float(self.repetition_rate)).__floor__() self.number_of_pulses = (
float(self.deposition_time) * float(self.repetition_rate)
).__floor__()
except ValueError: except ValueError:
# Since number_of_pulses is required, if it can't be calculated raise error: # Since number_of_pulses is required, if it can't be calculated raise error:
raise ValueError(""" raise ValueError("""
@@ -33,22 +39,32 @@ class Layer:
This has to be an error, since these fields are required by the NeXus standard. This has to be an error, since these fields are required by the NeXus standard.
Please edit your eLabFTW entry and retry. 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 = 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.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 = 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.process_pressure_unit = self.extra["Process pressure"]["unit"]
self.heating_method = self.extra["Heating Method"]["value"] self.heating_method = self.extra["Heating Method"]["value"]
self.layer_thickness = self.extra["Thickness"]["value"] self.layer_thickness = self.extra["Thickness"]["value"]
self.layer_thickness_unit = self.extra["Thickness"]["unit"] self.layer_thickness_unit = self.extra["Thickness"]["unit"]
self.buffer_gas = self.extra["Buffer gas"]["value"] self.buffer_gas = self.extra["Buffer gas"]["value"]
self.heater_target_distance = self.extra["Heater-target distance"]["value"] self.heater_target_distance = self.extra["Heater-target distance"]["value"]
self.heater_target_distance_unit = self.extra["Heater-target distance"]["unit"] self.heater_target_distance_unit = self.extra["Heater-target distance"][
self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity "unit"
]
self.laser_fluence = self.extra["Laser Intensity"][
"value"
] # here fluence = intensity
self.laser_fluence_unit = "J/(s cm^2)" self.laser_fluence_unit = "J/(s cm^2)"
self.laser_spot_area = self.extra["Spot Area"]["value"] self.laser_spot_area = self.extra["Spot Area"]["value"]
self.laser_spot_area_unit = "mm^2" self.laser_spot_area_unit = "mm^2"
try: try:
self.laser_energy = ( float(self.laser_fluence) * float(self.laser_spot_area) / 100 ).__round__(3) self.laser_energy = (
float(self.laser_fluence) * float(self.laser_spot_area) / 100
).__round__(3)
self.laser_energy_unit = "J/s" self.laser_energy_unit = "J/s"
except ValueError: except ValueError:
# Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution: # Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution:
@@ -61,39 +77,66 @@ class Layer:
self.laser_energy = "N/A" self.laser_energy = "N/A"
self.laser_energy_unit = "J/s" self.laser_energy_unit = "J/s"
# Laser rasternig section # Laser rasternig section
self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"]["value"] self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"][
self.laser_rastering_positions = self.extra["Laser Rastering Position"]["value"] "value"
self.laser_rastering_velocities = self.extra["Laser Rastering Speed"]["value"] ]
self.laser_rastering_positions = self.extra["Laser Rastering Position"][
"value"
]
self.laser_rastering_velocities = self.extra["Laser Rastering Speed"][
"value"
]
# Pre annealing section # Pre annealing section
self.pre_annealing_ambient_gas = self.extra["Buffer gas Pre"]["value"] self.pre_annealing_ambient_gas = self.extra["Buffer gas Pre"]["value"]
self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"] self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"]
self.pre_annealing_temperature = self.extra["Heater temperature Pre"]["value"] self.pre_annealing_temperature = self.extra["Heater temperature Pre"][
"value"
]
self.pre_annealing_duration = self.extra["Duration 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_pressure_unit = self.extra["Process pressure Pre"][
self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"]["unit"] "unit"
]
self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"][
"unit"
]
self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"] self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"]
# Post annealing section # Post annealing section
self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"] self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"]
self.post_annealing_pressure = self.extra["Process pressure 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_temperature = self.extra["Heater temperature PA"][
"value"
]
self.post_annealing_duration = self.extra["Duration 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_pressure_unit = self.extra["Process pressure PA"][
self.post_annealing_temperature_unit = self.extra["Heater temperature PA"]["unit"] "unit"
]
self.post_annealing_temperature_unit = self.extra["Heater temperature PA"][
"unit"
]
self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"] self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"]
# Rejected but suggested by the NeXus standard: # Rejected but suggested by the NeXus standard:
#self.laser_rastering_coefficients = None # self.laser_rastering_coefficients = None
except KeyError as k: except KeyError as k:
# Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # 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: # 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.") 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 # Optional
self.start_time = layer_data.get("created_at") or None self.start_time = layer_data.get("created_at") or None
self.description = layer_data.get("body") or None self.description = layer_data.get("body") or None
def get_instruments(self, apikey): def get_instruments(self, apikey):
raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(self.laser_system_elabid, entryType="items") raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(
raw_chamber_data = APIHandler(apikey).get_entry_from_elabid(self.chamber_elabid, entryType="items") self.laser_system_elabid, entryType="items"
raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid(self.rheed_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 = { instruments_used = {
"laser_system": raw_lasersys_data.get("title") or None, "laser_system": raw_lasersys_data.get("title") or None,
"deposition_chamber": raw_chamber_data.get("title") or None, "deposition_chamber": raw_chamber_data.get("title") or None,
@@ -101,31 +144,50 @@ class Layer:
} }
return instruments_used return instruments_used
# Three possible approaches for the next two methods: either return the raw data as retrieved from eLabFTW,
# or process it and return only the relevant information, or even simply return the list of filenames.
#
def fetch_textual_uploads(self, api_key):
""" """
return
def fetch_rheed_images(self, api_key):
return
class Entrypoint: class Entrypoint:
''' """
Entrypoint(sample_data) - where sample_data is a Python dictionary. Entrypoint(sample_data) - where sample_data is a Python dictionary.
Meant to be used for eLabFTW Resources of the "Sample" category. Meant to be used for eLabFTW Resources of the "Sample" category.
The entrypoint is the starting point of the process of resolving the data chain. The entrypoint is the starting point of the process of resolving the data chain.
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. 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.
''' """
def __init__(self, sample_data): def __init__(self, sample_data):
try: try:
self.extra = sample_data["metadata_decoded"]["extra_fields"] self.extra = sample_data["metadata_decoded"]["extra_fields"]
self.linked_items = sample_data["items_links"] # dict self.linked_items = sample_data["items_links"] # dict
self.batch_elabid = self.extra["Substrate batch"]["value"] # elabid self.batch_elabid = self.extra["Substrate batch"]["value"] # elabid
self.linked_experiments = sample_data["related_experiments_links"] # dict self.linked_experiments = sample_data["related_experiments_links"] # dict
self.linked_experiments_elabid = [ i["entityid"] for i in self.linked_experiments ] # list of elabid self.linked_experiments_elabid = [
i["entityid"] for i in self.linked_experiments
] # list of elabid
except KeyError as k: except KeyError as k:
# Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # 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: # 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 sample entry on eLabFTW and make sure you used the correct Resource template.") 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.'
)
# Non-required attributes: # Non-required attributes:
self.name = sample_data.get("title") or None # error prevention is more important than preventing empty fields here self.name = (
sample_data.get("title") or None
) # error prevention is more important than preventing empty fields here
class Material: class Material:
''' """
Material(material_data) - where material_data is a Python dictionary. Material(material_data) - where material_data is a Python dictionary.
Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories. Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories.
@@ -134,13 +196,16 @@ class Material:
* Name and formula; * Name and formula;
* Shape and dimensions; * Shape and dimensions;
* Misc. * Misc.
''' """
def __init__(self, material_data): def __init__(self, material_data):
try: try:
self.name = material_data["title"] # required self.name = material_data["title"] # required
self.extra = material_data["metadata_decoded"]["extra_fields"] self.extra = material_data["metadata_decoded"]["extra_fields"]
self.compound_elabid = self.extra["Compound"]["value"] self.compound_elabid = self.extra["Compound"]["value"]
self.dimensions = str(self.extra["Size"]["value"]) # strings have a .count() method self.dimensions = str(
self.extra["Size"]["value"]
) # strings have a .count() method
if self.dimensions.count("mm") == 2: if self.dimensions.count("mm") == 2:
self.dimensions_unit = "mm x mm" self.dimensions_unit = "mm x mm"
elif self.dimensions[-1] == '"': elif self.dimensions[-1] == '"':
@@ -150,23 +215,30 @@ class Material:
except KeyError as k: except KeyError as k:
# Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # 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: # 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 target/substrate entry on eLabFTW and make sure you used the correct Resource template.") 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.'
)
def get_compound_data(self, apikey): def get_compound_data(self, apikey):
raw_compound_data = APIHandler(apikey).get_entry_from_elabid(self.compound_elabid, entryType="items") raw_compound_data = APIHandler(apikey).get_entry_from_elabid(
self.compound_elabid, entryType="items"
)
name = raw_compound_data["title"] name = raw_compound_data["title"]
extra = raw_compound_data["metadata_decoded"]["extra_fields"] extra = raw_compound_data["metadata_decoded"]["extra_fields"]
formula = extra.get("Chemical formula") formula = extra.get("Chemical formula")
cas = extra.get("CAS number ") or { "value": None } cas = extra.get("CAS number ") or {"value": None}
compound_data = { compound_data = {
"name" : name, "name": name,
"chemical_formula" : formula.get("value"), "chemical_formula": formula.get("value"),
"cas_number" : cas.get("value") "cas_number": cas.get("value"),
} }
return compound_data return compound_data
def get_compound_formula(self, apikey): def get_compound_formula(self, apikey):
formula = self.get_compound_data(apikey).get("chemical_formula") formula = self.get_compound_data(apikey).get("chemical_formula")
return formula return formula
class Substrate(Material): class Substrate(Material):
def __init__(self, material_data): def __init__(self, material_data):
super().__init__(material_data) super().__init__(material_data)
@@ -176,13 +248,16 @@ class Substrate(Material):
self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"] self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"]
self.miscut_direction = self.extra["Miscut Direction"]["value"] self.miscut_direction = self.extra["Miscut Direction"]["value"]
# Not present (yet) on eLabFTW for Substrates: # Not present (yet) on eLabFTW for Substrates:
self.thickness = "" #self.extra["Thickness"]["value"] self.thickness = "" # self.extra["Thickness"]["value"]
self.thickness_unit = "μm" #self.extra["Thickness"]["unit"] self.thickness_unit = "μm" # self.extra["Thickness"]["unit"]
self.surface_treatment = self.extra["Surface treatment"]["value"] self.surface_treatment = self.extra["Surface treatment"]["value"]
self.manufacturer = self.extra["Supplier"]["value"] self.manufacturer = self.extra["Supplier"]["value"]
self.batch_id = self.extra["Batch ID"]["value"] self.batch_id = self.extra["Batch ID"]["value"]
except KeyError as k: except KeyError as k:
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.") 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.'
)
class Target(Material): class Target(Material):
def __init__(self, material_data): def __init__(self, material_data):
@@ -194,13 +269,15 @@ class Target(Material):
self.solid_form = self.extra["Solid form"]["value"] self.solid_form = self.extra["Solid form"]["value"]
self.manufacturer = self.extra["Supplier"]["value"] self.manufacturer = self.extra["Supplier"]["value"]
except KeyError as k: 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.") 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: # Non-required attributes:
self.description = material_data.get("body") or "" self.description = material_data.get("body") or ""
if __name__ == "__main__":
if __name__=="__main__": head = APIHandler("MyApiKey-123456789abcdef")
head = Header("MyApiKey-123456789abcdef")
print(f"Example header:\n\t{head.header}\n") print(f"Example header:\n\t{head.header}\n")
print("Warning: you're not supposed to be running this as the main program.") print("Warning: you're not supposed to be running this as the main program.")