Loading src/tgreft/utils/data/dataloader.py +46 −24 Original line number Diff line number Diff line from refl1d.names import * from refl1d.names import ( Slab, SLD, ) class DataLoader: """Add description of the class here""" def __init__(self, json_dict: dict): default_dict = { "parameters": { "q_min": 0.008, "q_max": 0.2, "step_size": 0.015, "FINAL_SEI_SLD": 6.13, "SIMULATE_ERRORS": True, "ERR": 0.15, "total_time": 50, "transition_time": 3, "transition_midpoint": 15, } } def __init__(self, input_dict: dict): """Initialize the class. Parameters ---------- json_dict : json dictionary json dictionary of all parameters and materials to stack in a sample. input_dict : dictionary Dictionary of all parameters and materials to stack in a sample. """ self.json_dict = json_dict self.q_min = json_dict["parameters"]["q_min"] self.q_max = json_dict["parameters"]["q_max"] self.step_size = json_dict["parameters"]["step"] self.final_sei_sld = json_dict["parameters"]["FINAL_SEI_SLD"] self.simulate_errors = json_dict["parameters"]["SIMULATE_ERRORS"] self.err = json_dict["parameters"]["ERR"] self.total_time = json_dict["parameters"]["total_time"] self.transition_time = json_dict["parameters"]["transition_time"] self.transition_midpoint = json_dict["parameters"]["transition_midpoint"] self.sample = self.create_sample_from_json(json_dict["materials"]) def create_slab_chunk(self, material : dict) -> "Slab": self.param = input_dict.get("parameters", self.default_dict["parameters"]) if self.param: self.q_min = self.param.get("q_min", self.default_dict["parameters"]["q_min"]) self.q_max = self.param.get("q_max", self.default_dict["parameters"]["q_max"]) self.step_size = self.param.get("step_size", self.default_dict["parameters"]["step_size"]) self.final_sei_sld = self.param.get("FINAL_SEI_SLD", self.default_dict["parameters"]["FINAL_SEI_SLD"]) self.simulate_errors = self.param.get("SIMULATE_ERRORS", self.default_dict["parameters"]["SIMULATE_ERRORS"]) self.err = self.param.get("ERR", self.default_dict["parameters"]["ERR"]) self.total_time = self.param.get("total_time", self.default_dict["parameters"]["total_time"]) self.transition_time = self.param.get("transition_time", self.default_dict["parameters"]["transition_time"]) self.transition_midpoint = self.param.get( "transition_midpoint", self.default_dict["parameters"]["transition_midpoint"] ) self.sample = self.create_sample_from_dict(input_dict.get("materials")) def create_slab_chunk(self, material: dict) -> "Slab": """Return a slab chunk built from given configuration. Parameters Loading @@ -49,8 +72,7 @@ class DataLoader: return slab def create_sample_from_json(self, json_object : list) -> "Slab | Stack": def create_sample_from_dict(self, input_dict: list) -> Slab: """Return a slab instance built from given configuration. Parameters Loading @@ -64,8 +86,8 @@ class DataLoader: The slab instance. """ sample = self.create_slab_chunk(json_object[0]) for i in range(1, len(json_object)): sample = sample | self.create_slab_chunk(json_object[i]) sample = self.create_slab_chunk(input_dict[0]) for i in range(1, len(input_dict)): sample = sample | self.create_slab_chunk(input_dict[i]) return sample src/tgreft/utils/data/r_curve_generator.py +152 −142 Original line number Diff line number Diff line Loading @@ -3,14 +3,13 @@ import json import numpy as np import math from refl1d.names import * from refl1d.names import QProbe, Experiment from dataloader import DataLoader class RCurveGenerator: class RCurveGenerator: def __init__(self, data: DataLoader): """Initialize the class. Parameters Loading @@ -20,14 +19,72 @@ class RCurveGenerator: """ self.data = data self.probe, self.tr_probe = self.create_probes(data.q_min, data.q_max, res=data.step) self.probe, self.tr_probe = create_probes(data.q_min, data.q_max, data.step_size) self.expt = Experiment(probe=self.probe, sample=self.data.sample) self.r_final, self.r_init = self.get_states(self.expt, self.data.final_sei_sld, self.data.simulate_errors, self.data.err) self.r_final, self.r_init = get_states( self.expt, self.data.final_sei_sld, self.data.simulate_errors, self.data.err ) self.tr_expt = Experiment(probe=self.tr_probe, sample=self.data.sample) self.tr_data, self.rho_data = self.generate_tNR(self.tr_expt, self.data.total_time, self.data.transition_time, self.data.transition_midpoint, self.data.final_sei_sld, self.data.simulate_errors, self.data.err) self.tr_data, self.rho_data = generate_tNR( self.tr_expt, self.data.total_time, self.data.transition_time, self.data.transition_midpoint, self.data.final_sei_sld, self.data.simulate_errors, self.data.err, ) @property def get_r_final(self) -> list: """Returns a list from the RCurveGenerator object instance. Returns ------- list r_final list """ return self.r_final def create_probes(self, q_min : float, q_max : float, step_size : float, resolution : float = 0.028) -> tuple: @property def get_r_init(self) -> list: """Returns a list from the object instance. Returns ------- list r_init list """ return self.r_init @property def get_tr_data(self) -> list: """Returns a list from the object instance. Returns ------- list tr_data list """ return self.tr_data @property def get_rho_data(self) -> list: """Returns a list from the object instance. Returns ------- list rho_data list """ return self.rho_data def create_probes(q_min: float, q_max: float, step_size: float, resolution: float = 0.028) -> tuple: """Returns two probes, one using the full data and one with a slice, in the form of a tuple. Parameters Loading Loading @@ -65,8 +122,8 @@ class RCurveGenerator: return probe, tr_probe def get_states(self, expt, final_sei_sld, simulate_errors, err) -> tuple: def get_states(expt: Experiment, final_sei_sld: float, simulate_errors: bool, err: float) -> tuple: """Returns a tuple containing both the initial and final r states. Parameters Loading @@ -91,9 +148,8 @@ class RCurveGenerator: if simulate_errors: r_final = np.random.normal(r_final, err * r_final) # Initial state ################################################################ expt.sample['SEI'].material.rho.value = final_sei_sld expt.sample["SEI"].material.rho.value = final_sei_sld expt.update() _, r_init = expt.reflectivity() if simulate_errors: Loading @@ -101,7 +157,16 @@ class RCurveGenerator: return r_final, r_init def generate_tNR(self, tr_expt, total_time, transition_time, transition_midpoint, final_sei_sld, simulate_errors, err) -> tuple: def generate_tNR( tr_expt: Experiment, total_time: int, transition_time: int, transition_midpoint: int, final_sei_sld: float, simulate_errors: bool, err: float, ) -> tuple: """Return a tuple built containing tr_data and rho_data. Parameters Loading Loading @@ -130,9 +195,11 @@ class RCurveGenerator: rho_data = [] for i in range(total_time): # This is a simple ERF transition, but it could be any function! rho_sei = final_sei_sld - (final_sei_sld-4.581) * (1 + math.erf((i-transition_midpoint)/transition_time)) / 2 rho_sei = ( final_sei_sld - (final_sei_sld - 4.581) * (1 + math.erf((i - transition_midpoint) / transition_time)) / 2 ) tr_expt.sample['SEI'].material.rho.value = rho_sei tr_expt.sample["SEI"].material.rho.value = rho_sei tr_expt.update() _, _r = tr_expt.reflectivity() if simulate_errors: Loading @@ -144,67 +211,10 @@ class RCurveGenerator: tr_data = np.asarray(tr_data) return tr_data, rho_data def get_r_final(self) -> list: """Returns a list from the RCurveGenerator object instance. Returns ------- list r_final list """ return self.r_final def get_r_init(self) -> list: """Returns a list from the object instance. Returns ------- list r_init list """ return self.r_init def get_tr_data(self) -> list: """Returns a list from the object instance. Returns ------- list tr_data list """ return self.tr_data def get_rho_data(self) -> list: """Returns a list from the object instance. Returns ------- list rho_data list """ return self.rho_data """ USE EXAMPLE if __name__ == "__main__": f = open("data.json", "r") data = json.load(f) dataloader = DataLoader(data) rc = RCurveGenerator(dataloader) print(rc.get_r_init()) #gen = RCurveGenerator(0.008, 0.2) #print(gen.q) """ print(rc.get_r_init) Loading
src/tgreft/utils/data/dataloader.py +46 −24 Original line number Diff line number Diff line from refl1d.names import * from refl1d.names import ( Slab, SLD, ) class DataLoader: """Add description of the class here""" def __init__(self, json_dict: dict): default_dict = { "parameters": { "q_min": 0.008, "q_max": 0.2, "step_size": 0.015, "FINAL_SEI_SLD": 6.13, "SIMULATE_ERRORS": True, "ERR": 0.15, "total_time": 50, "transition_time": 3, "transition_midpoint": 15, } } def __init__(self, input_dict: dict): """Initialize the class. Parameters ---------- json_dict : json dictionary json dictionary of all parameters and materials to stack in a sample. input_dict : dictionary Dictionary of all parameters and materials to stack in a sample. """ self.json_dict = json_dict self.q_min = json_dict["parameters"]["q_min"] self.q_max = json_dict["parameters"]["q_max"] self.step_size = json_dict["parameters"]["step"] self.final_sei_sld = json_dict["parameters"]["FINAL_SEI_SLD"] self.simulate_errors = json_dict["parameters"]["SIMULATE_ERRORS"] self.err = json_dict["parameters"]["ERR"] self.total_time = json_dict["parameters"]["total_time"] self.transition_time = json_dict["parameters"]["transition_time"] self.transition_midpoint = json_dict["parameters"]["transition_midpoint"] self.sample = self.create_sample_from_json(json_dict["materials"]) def create_slab_chunk(self, material : dict) -> "Slab": self.param = input_dict.get("parameters", self.default_dict["parameters"]) if self.param: self.q_min = self.param.get("q_min", self.default_dict["parameters"]["q_min"]) self.q_max = self.param.get("q_max", self.default_dict["parameters"]["q_max"]) self.step_size = self.param.get("step_size", self.default_dict["parameters"]["step_size"]) self.final_sei_sld = self.param.get("FINAL_SEI_SLD", self.default_dict["parameters"]["FINAL_SEI_SLD"]) self.simulate_errors = self.param.get("SIMULATE_ERRORS", self.default_dict["parameters"]["SIMULATE_ERRORS"]) self.err = self.param.get("ERR", self.default_dict["parameters"]["ERR"]) self.total_time = self.param.get("total_time", self.default_dict["parameters"]["total_time"]) self.transition_time = self.param.get("transition_time", self.default_dict["parameters"]["transition_time"]) self.transition_midpoint = self.param.get( "transition_midpoint", self.default_dict["parameters"]["transition_midpoint"] ) self.sample = self.create_sample_from_dict(input_dict.get("materials")) def create_slab_chunk(self, material: dict) -> "Slab": """Return a slab chunk built from given configuration. Parameters Loading @@ -49,8 +72,7 @@ class DataLoader: return slab def create_sample_from_json(self, json_object : list) -> "Slab | Stack": def create_sample_from_dict(self, input_dict: list) -> Slab: """Return a slab instance built from given configuration. Parameters Loading @@ -64,8 +86,8 @@ class DataLoader: The slab instance. """ sample = self.create_slab_chunk(json_object[0]) for i in range(1, len(json_object)): sample = sample | self.create_slab_chunk(json_object[i]) sample = self.create_slab_chunk(input_dict[0]) for i in range(1, len(input_dict)): sample = sample | self.create_slab_chunk(input_dict[i]) return sample
src/tgreft/utils/data/r_curve_generator.py +152 −142 Original line number Diff line number Diff line Loading @@ -3,14 +3,13 @@ import json import numpy as np import math from refl1d.names import * from refl1d.names import QProbe, Experiment from dataloader import DataLoader class RCurveGenerator: class RCurveGenerator: def __init__(self, data: DataLoader): """Initialize the class. Parameters Loading @@ -20,14 +19,72 @@ class RCurveGenerator: """ self.data = data self.probe, self.tr_probe = self.create_probes(data.q_min, data.q_max, res=data.step) self.probe, self.tr_probe = create_probes(data.q_min, data.q_max, data.step_size) self.expt = Experiment(probe=self.probe, sample=self.data.sample) self.r_final, self.r_init = self.get_states(self.expt, self.data.final_sei_sld, self.data.simulate_errors, self.data.err) self.r_final, self.r_init = get_states( self.expt, self.data.final_sei_sld, self.data.simulate_errors, self.data.err ) self.tr_expt = Experiment(probe=self.tr_probe, sample=self.data.sample) self.tr_data, self.rho_data = self.generate_tNR(self.tr_expt, self.data.total_time, self.data.transition_time, self.data.transition_midpoint, self.data.final_sei_sld, self.data.simulate_errors, self.data.err) self.tr_data, self.rho_data = generate_tNR( self.tr_expt, self.data.total_time, self.data.transition_time, self.data.transition_midpoint, self.data.final_sei_sld, self.data.simulate_errors, self.data.err, ) @property def get_r_final(self) -> list: """Returns a list from the RCurveGenerator object instance. Returns ------- list r_final list """ return self.r_final def create_probes(self, q_min : float, q_max : float, step_size : float, resolution : float = 0.028) -> tuple: @property def get_r_init(self) -> list: """Returns a list from the object instance. Returns ------- list r_init list """ return self.r_init @property def get_tr_data(self) -> list: """Returns a list from the object instance. Returns ------- list tr_data list """ return self.tr_data @property def get_rho_data(self) -> list: """Returns a list from the object instance. Returns ------- list rho_data list """ return self.rho_data def create_probes(q_min: float, q_max: float, step_size: float, resolution: float = 0.028) -> tuple: """Returns two probes, one using the full data and one with a slice, in the form of a tuple. Parameters Loading Loading @@ -65,8 +122,8 @@ class RCurveGenerator: return probe, tr_probe def get_states(self, expt, final_sei_sld, simulate_errors, err) -> tuple: def get_states(expt: Experiment, final_sei_sld: float, simulate_errors: bool, err: float) -> tuple: """Returns a tuple containing both the initial and final r states. Parameters Loading @@ -91,9 +148,8 @@ class RCurveGenerator: if simulate_errors: r_final = np.random.normal(r_final, err * r_final) # Initial state ################################################################ expt.sample['SEI'].material.rho.value = final_sei_sld expt.sample["SEI"].material.rho.value = final_sei_sld expt.update() _, r_init = expt.reflectivity() if simulate_errors: Loading @@ -101,7 +157,16 @@ class RCurveGenerator: return r_final, r_init def generate_tNR(self, tr_expt, total_time, transition_time, transition_midpoint, final_sei_sld, simulate_errors, err) -> tuple: def generate_tNR( tr_expt: Experiment, total_time: int, transition_time: int, transition_midpoint: int, final_sei_sld: float, simulate_errors: bool, err: float, ) -> tuple: """Return a tuple built containing tr_data and rho_data. Parameters Loading Loading @@ -130,9 +195,11 @@ class RCurveGenerator: rho_data = [] for i in range(total_time): # This is a simple ERF transition, but it could be any function! rho_sei = final_sei_sld - (final_sei_sld-4.581) * (1 + math.erf((i-transition_midpoint)/transition_time)) / 2 rho_sei = ( final_sei_sld - (final_sei_sld - 4.581) * (1 + math.erf((i - transition_midpoint) / transition_time)) / 2 ) tr_expt.sample['SEI'].material.rho.value = rho_sei tr_expt.sample["SEI"].material.rho.value = rho_sei tr_expt.update() _, _r = tr_expt.reflectivity() if simulate_errors: Loading @@ -144,67 +211,10 @@ class RCurveGenerator: tr_data = np.asarray(tr_data) return tr_data, rho_data def get_r_final(self) -> list: """Returns a list from the RCurveGenerator object instance. Returns ------- list r_final list """ return self.r_final def get_r_init(self) -> list: """Returns a list from the object instance. Returns ------- list r_init list """ return self.r_init def get_tr_data(self) -> list: """Returns a list from the object instance. Returns ------- list tr_data list """ return self.tr_data def get_rho_data(self) -> list: """Returns a list from the object instance. Returns ------- list rho_data list """ return self.rho_data """ USE EXAMPLE if __name__ == "__main__": f = open("data.json", "r") data = json.load(f) dataloader = DataLoader(data) rc = RCurveGenerator(dataloader) print(rc.get_r_init()) #gen = RCurveGenerator(0.008, 0.2) #print(gen.q) """ print(rc.get_r_init)
