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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,196 +1,133 @@ | ||
| from datetime import datetime | ||
| from typing import Optional | ||
|
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| import numpy as np | ||
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| class NexusDict(object): | ||
| """Read in dictionaries from DAS logs, instrument configuration json or sample json, | ||
| format into NeXus style: nxentry_dict = {"attrs":{"attr1":attr1, ...}, "dataset":dataset} | ||
| Attributes: | ||
| daslogs_dict (dict) | ||
| instrument_dict (dict) | ||
| sample_dict (dict) | ||
| nxentry_dict (dict) | ||
| Methods: | ||
| set_attrs() | ||
| get_attrs() | ||
| get_dataset() | ||
| set_dataset() | ||
| """ | ||
|
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| def __init__( | ||
| self, | ||
| daslogs_dict: Optional[dict] = None, | ||
| instrument_dict: Optional[dict] = None, | ||
| sample_dict: Optional[dict] = None, | ||
| ) -> None: | ||
| self.daslogs_dict = daslogs_dict | ||
| self.instrument_dict = instrument_dict | ||
| self.sample_dict = sample_dict | ||
| self.nxentry_dict: dict = {"attrs": {}} | ||
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| def set_attrs(self, **kwargs): | ||
| for k, v in kwargs.items(): | ||
| self.nxentry_dict["attrs"].update({k: v}) | ||
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| def get_attrs(self, key: str, default=None): | ||
| val = self.nxentry_dict["attrs"].get(key) | ||
| return val if val is not None else default | ||
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| def get_dataset(self, key: str, default=None): | ||
| val = self.nxentry_dict.get(key) | ||
| return val["dataset"] if val is not None else default | ||
|
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| def set_dataset(self, key: str, dataset: str | dict | np.ndarray, **kwargs): | ||
| """Set dataset with proper format if dataset is a string or an array. Take directly if dictionary.""" | ||
|
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| def _add_dataset_entry( | ||
| entry_dict: dict, | ||
| key: str, | ||
| daslogs: dict, | ||
| daslogs_key: Optional[str] = None, | ||
| **kwargs, | ||
| ): | ||
| key = key if daslogs_key is None else daslogs_key | ||
| try: | ||
| val = daslogs[key] | ||
| entry_dict.update({key: {"dataset": val}}) | ||
| if not kwargs: | ||
| return entry_dict | ||
| attr_dict = {} | ||
| for k, v in kwargs.items(): | ||
| attr_dict.update({k: v}) | ||
| entry_dict[key].update({"attrs": attr_dict}) | ||
| return entry_dict | ||
|
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||
| except KeyError: | ||
| print(f"Variable {key} cannot be found in DAS logs.") | ||
| return entry_dict | ||
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| def nxsource(spicelogs, instrument_config_params): | ||
| source = { | ||
| "attrs": {"NX_class": "NXsource", "EX_required": "true"}, | ||
| "name": { | ||
| "attrs": {"type": "NX_CHAR", "EX_required": "true"}, | ||
| "dataset": "HFIR", | ||
| }, | ||
| "probe": { | ||
| "attrs": {"type": "NX_CHAR", "EX_required": "true"}, | ||
| "dataset": "neutron", | ||
| }, | ||
| } | ||
| if "type" in kwargs.keys(): | ||
| match kwargs["type"]: | ||
| case "NX_CHAR": | ||
| dataset = str(dataset) | ||
| case "NX_INT": | ||
| dataset = dataset | ||
| case "NX_FLOAT": | ||
| dataset = dataset | ||
|
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| self.nxentry_dict.update({key: {"dataset": dataset}}) | ||
| self.nxentry_dict[key].update({"attrs": attr_dict}) | ||
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| def set_dataset_from( | ||
| self, | ||
| key: str, | ||
| source: Literal["DAS_DATA", "DAS_METADATA", "INSTRU", "SAMPLE"] = "DAS_DATA", | ||
| daslogs_key: Optional[str] = None, | ||
| **kwargs, | ||
| ): | ||
| match source: | ||
| case "DAS_DATA": | ||
| if self.daslogs_dict is None: | ||
| raise ValueError("Cannot find DAS logs.") | ||
| case "DAS_METADATA": | ||
| if self.daslogs_dict is None: | ||
| raise ValueError("Cannot find DAS logs.") | ||
| case "INSTRU": | ||
| if self.instrument_dict is None: | ||
| raise ValueError("Cannot find instrument configuration dict.") | ||
| case "SMAPLE": | ||
| if self.sample_config_params is None: | ||
| raise ValueError("Cannot find sample configuration dict.") | ||
| case _: | ||
| raise ValueError(f"Unrecogonized source {source}.") | ||
|
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| match source: | ||
| case "DAS_DATA": | ||
| try: | ||
| val = self.daslogs_dict[key] if daslogs_key is None else self.daslogs_dict[daslogs_key] | ||
| except KeyError: | ||
| print(f"Variable {key} cannot be found in DAS logs.") | ||
| return self.nxentry_dict | ||
|
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| self.nxentry_dict.update({key: val}) | ||
| if not kwargs: | ||
| return self.nxentry_dict | ||
|
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| attr_dict = {} | ||
| for k, v in kwargs.items(): | ||
| attr_dict.update({k: v}) | ||
| self.nxentry_dict[key].update({"attrs": attr_dict}) | ||
| return self.nxentry_dict | ||
| case "DAS_METADATA": | ||
| pass | ||
| case "INSTRU": | ||
| pass | ||
| case "SMAPLE": | ||
| pass | ||
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| def spicelogs_to_nested_dict( | ||
| spicelogs: dict, | ||
| instrument_dict: Optional[dict], | ||
| sample_dict: Optional[dict], | ||
| ) -> dict: | ||
|
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| nxsource = NexusDict() | ||
| nxsource.set_attrs(NX_class="NXsource", EX_required="true") | ||
| nxsource.set_dataset(key="name", dataset="HFIR", type="NX_CHAR", EX_required="true") | ||
| nxsource.set_dataset(key="probe", dataset="neutron", type="NX_CHAR", EX_required="true") | ||
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| # Effective distance from sample Distance as seen by radiation from sample. | ||
| # This number should be negative to signify that it is upstream of the sample. | ||
| # nxsource.attrs["distance"] = -0.0 | ||
| return source | ||
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| def nxmono(spicelogs, instrument_config_params): | ||
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| mono = {"attrs": {"NX_class": "NXcrystal", "EX_required": "true"}} | ||
| mono = _add_dataset_entry(mono, key="ei", daslogs=spicelogs, type="NX_FLOAT", EX_required="true", unit="meV") | ||
| mono.update({"type": {"dataset": spicelogs["attrs"]["monochromator"], "attrs": {"type": "NX_CHAR"}}}) | ||
| mono.update({"sense": {"dataset": spicelogs["attrs"]["sense"][0], "attrs": {"type": "NX_CHAR"}}}) | ||
| mono = _add_dataset_entry(mono, key="m1", daslogs=spicelogs, type="NX_FLOAT", unit="degrees") | ||
| mono = _add_dataset_entry(mono, key="m2", daslogs=spicelogs, type="NX_FLOAT", unit="degrees") | ||
| mono = _add_dataset_entry(mono, key="mfocus", daslogs=spicelogs, type="NX_FLOAT") | ||
| mono = _add_dataset_entry(mono, key="marc", daslogs=spicelogs, type="NX_FLOAT") | ||
| mono = _add_dataset_entry(mono, key="mtrans", daslogs=spicelogs, type="NX_FLOAT") | ||
| mono = _add_dataset_entry(mono, key="focal_length", daslogs=spicelogs, type="NX_FLOAT") | ||
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| return mono | ||
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| def nxcoll(spicelogs, instrument_config_params): | ||
| pass | ||
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| def nxana(spicelogs, instrument_config_params): | ||
| ana = {"attrs": {"NX_class": "NXcrystal", "EX_required": "true"}} | ||
| ana = _add_dataset_entry(ana, key="ef", daslogs=spicelogs, type="NX_FLOAT", EX_required="true", unit="meV") | ||
| ana.update({"type": {"dataset": spicelogs["attrs"]["analyzer"], "attrs": {"type": "NX_CHAR"}}}) | ||
| ana.update({"sense": {"dataset": spicelogs["attrs"]["sense"][2], "attrs": {"type": "NX_CHAR"}}}) | ||
| ana = _add_dataset_entry(ana, key="a1", daslogs=spicelogs, type="NX_FLOAT", unit="degrees") | ||
| ana = _add_dataset_entry(ana, key="a2", daslogs=spicelogs, type="NX_FLOAT", unit="degrees") | ||
| ana = _add_dataset_entry(ana, key="afocus", daslogs=spicelogs, type="NX_FLOAT") | ||
| for i in range(8): | ||
| ana = _add_dataset_entry(ana, key=f"qm{i+1}", daslogs=spicelogs, type="NX_FLOAT") | ||
| ana = _add_dataset_entry(ana, key=f"xm{i+1}", daslogs=spicelogs, type="NX_FLOAT") | ||
| return ana | ||
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| def nxdet(spicelogs, instrument_config_params): | ||
| det = {"attrs": {"NX_class": "NXdetector", "EX_required": "true"}} | ||
| det = _add_dataset_entry(det, key="detector", daslogs=spicelogs, type="NX_INT", EX_required="true", unit="counts") | ||
| # polar_angle | ||
| return det | ||
|
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|
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| def nxmonitor(spicelogs, instrument_config_params): | ||
| monitor = {"attrs": {"NX_class": "NXmonitor", "EX_required": "true"}} | ||
| preset_type = spicelogs["attrs"]["preset_type"] | ||
| match preset_type: | ||
| case "countfile": # polarization data | ||
| print("Countfile preset type is not supported.") | ||
|
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||
| case "normal": | ||
| preset_channel = spicelogs["attrs"]["preset_channel"] | ||
| monitor.update({"mode": {"dataset": preset_channel, "attrs": {"type": "NX_CHAR", "EX_required": "true"}}}) | ||
| monitor.update( | ||
| { | ||
| "preset": { | ||
| "dataset": spicelogs["attrs"]["preset_value"], | ||
| "attrs": {"type": "NX_FLOAT", "EX_required": "true"}, | ||
| } | ||
| } | ||
| ) | ||
| monitor = _add_dataset_entry(monitor, key="time", daslogs=spicelogs, type="NX_FLOAT", units="seconds") | ||
| monitor = _add_dataset_entry(monitor, key="monitor", daslogs=spicelogs, type="NX_INT", units="counts") | ||
| monitor = _add_dataset_entry(monitor, key="mcu", daslogs=spicelogs, type="NX_FLOAT") | ||
| monitor_data_dict = monitor[preset_channel] | ||
| monitor.update({"data": monitor_data_dict}) | ||
|
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| case _: | ||
| print(f"Unrecogonized preset type {preset_type}.") | ||
|
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| return monitor | ||
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| def nxsample(spicelogs, sample_config_params): | ||
| return {} | ||
|
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| nxmono = NexusDict(daslogs_dict=spicelogs) | ||
| nxmono.set_attrs(NX_class="NXcrystal", EX_required="true") | ||
| # nxmono.set_dataset_from(source="DAS_DATA", key="ei", type="NX_FLOAT", EX_required="true", unit="meV") | ||
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| def nxslit(spicelogs, instrument_config_params): | ||
| return {} | ||
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| def nxflipper(spicelogs, instrument_config_params): | ||
| return {} | ||
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| def _spicelogs_to_nexus(spicelogs, instrument_config_params, sample_config_params): | ||
| metadata = spicelogs["attrs"] | ||
| # TODO timezone | ||
| start_date_time = "{} {}".format(metadata["date"], metadata["time"]) | ||
| start_time = datetime.strptime(start_date_time, "%m/%d/%Y %I:%M:%S %p").isoformat() | ||
| # if "end_time" in das_logs.attrs: # last scan never finished | ||
| end_date_time = metadata["end_time"] | ||
| end_time = datetime.strptime(end_date_time, "%m/%d/%Y %I:%M:%S %p").isoformat() | ||
|
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| scan_dict = { | ||
| "attrs": { | ||
| "NX_class": "NXentry", | ||
| "EX_required": "true", | ||
| }, | ||
| "SPICElogs": spicelogs, | ||
| "definition": { | ||
| "attrs": {"EX_required": "true", "type": "NX_CHAR"}, | ||
| "dataset": "NXtas", | ||
| }, | ||
| "title": { | ||
| "attrs": {"EX_required": "true", "type": "NX_CHAR"}, | ||
| "dataset": metadata["scan_title"], | ||
| }, | ||
| "start_time": { | ||
| "attrs": {"EX_required": "true", "type": "NX_DATE_TIME"}, | ||
| "dataset": start_time, | ||
| }, | ||
| "end_time": { | ||
| "attrs": {"type": "NX_DATE_TIME"}, | ||
| "dataset": end_time, | ||
| }, | ||
| "instrument": { | ||
| "attrs": {"EX_required": "true", "NX_class": "NXinstrument"}, | ||
| "name": {"attrs": {"type": "NX_CHAR"}, "dataset": metadata["instrument"]}, | ||
| "source": nxsource(spicelogs, instrument_config_params), | ||
| "collimator": nxcoll(spicelogs, instrument_config_params), | ||
| "monochromator": nxmono(spicelogs, instrument_config_params), | ||
| "analyser": nxana(spicelogs, instrument_config_params), | ||
| "detector": nxdet(spicelogs, instrument_config_params), | ||
| "slit": nxslit(spicelogs, instrument_config_params), | ||
| "flipper": nxflipper(spicelogs, instrument_config_params), | ||
| }, | ||
| "monitor": nxmonitor(spicelogs, instrument_config_params), | ||
| "sample": nxsample(spicelogs, sample_config_params), | ||
| "data": {}, | ||
| } | ||
| return scan_dict | ||
|
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| def daslogs_to_nexus_dict( | ||
| daslogs: dict, | ||
| instrument_config_params: Optional[str], | ||
| sample_config_params: Optional[str], | ||
| ) -> dict: | ||
| """Format DASlogs dict into NeXus dict""" | ||
|
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| match (das_key := tuple(daslogs.keys())[0]): | ||
| case "SPICElogs": | ||
| scan_dict = _spicelogs_to_nexus( | ||
| daslogs["SPICElogs"], | ||
| instrument_config_params, | ||
| sample_config_params, | ||
| ) | ||
| case _: | ||
| raise KeyError(f"Unrecogonized DASlogs key {das_key}.") | ||
|
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| return scan_dict |
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