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implemeting nxdict group
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Bing Li committed Sep 26, 2024
1 parent 526882e commit 9143b19
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Showing 4 changed files with 104 additions and 35 deletions.
107 changes: 78 additions & 29 deletions src/tavi/data/nxdict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,30 @@
from typing import Optional


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

except KeyError:
print(f"Variable {key} cannot be found in DAS logs.")
return entry_dict


def nxsource(spicelogs, instrument_config_params):
source = {
"attrs": {"NX_class": "NXsource", "EX_required": "true"},
Expand All @@ -21,49 +45,74 @@ def nxsource(spicelogs, instrument_config_params):


def nxmono(spicelogs, instrument_config_params):
metadata = spicelogs["attrs"]

try:
mono = {
"attrs": {"NX_class": "NXcrystal", "EX_required": "true"},
"ei": {
"dataset": spicelogs["ei"],
"attrs": {"type": "NX_FLOAT", "EX_required": "true", "units": "meV"},
},
"type": {"dataset": metadata["monochromator"], "attrs": {"type": "NX_CHAR"}},
"sense": {"dataset": metadata["sense"][0], "attrs": {"type": "NX_CHAR"}},
"m1": {
"dataset": spicelogs["m1"],
"attrs": {"type": "NX_FLOAT", "units": "degrees"},
},
"m2": {
"dataset": spicelogs["m2"],
"attrs": {"type": "NX_FLOAT", "units": "degrees"},
},
"mfocus": {"dataset": spicelogs["mfocus"], "attrs": {"type": "NX_FLOAT"}},
"marc": {"dataset": spicelogs["marc"], "attrs": {"type": "NX_FLOAT"}},
"mtrans": {"dataset": spicelogs["mtrans"], "attrs": {"type": "NX_FLOAT"}},
"focal_length": {"dataset": spicelogs["focal_length"], "attrs": {"type": "NX_FLOAT"}},
}
except KeyError:
pass
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")

return mono


def nxcoll(spicelogs, instrument_config_params):
return {}
pass


def nxana(spicelogs, instrument_config_params):
return {}
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


def nxdet(spicelogs, instrument_config_params):
return {}
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


def nxmonitor(spicelogs, instrument_config_params):
return {}
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.")

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})

case _:
print(f"Unrecogonized preset type {preset_type}.")

return monitor


def nxsample(spicelogs, sample_config_params):
Expand Down
30 changes: 25 additions & 5 deletions src/tavi/data/nxentry.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from typing import Optional

import h5py
import numpy as np

from tavi.data.spice_reader import spice_data_reader

Expand Down Expand Up @@ -50,6 +51,27 @@ def _write_recursively(items, nexus_entry):
string encoded with utf-8
"""

def format_dataset(value):
"""format if type is given in attributes"""
dv = value["dataset"]

if attr := value.get("attrs"):
attr_type = attr.get("type")
match attr_type:
case "NX_CHAR":
dv = dv.encode("utf-8")
case "NX_FLOAT":
dv = np.array(dv).astype("float")
case "NX_INT":
dv = np.array(dv).astype("int")
case "NX_DATE_TIME":
pass
case _:
if isinstance(dv, str):
dv = dv.encode("utf-8")
print(dv)
return dv

for key, value in items.items():
if key == "attrs":
for attr_key, attr_value in value.items():
Expand All @@ -59,13 +81,11 @@ def _write_recursively(items, nexus_entry):
else:
if isinstance(value, dict):
if "dataset" in value.keys():
dv = value["dataset"]
if isinstance(dv, str):
dv = dv.encode("utf-8")
if key in nexus_entry:
dv = format_dataset(value)
if key in nexus_entry: # dataset exists
ds = nexus_entry[key]
ds[...] = dv
else:
else: # create dataset
ds = nexus_entry.create_dataset(name=key, data=dv, maxshape=None)
NexusEntry._write_recursively(value, ds)
else:
Expand Down
2 changes: 1 addition & 1 deletion src/tavi/data/scan_old/spice_to_nexus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -514,7 +514,7 @@ def _nexus_coll(nxcoll, das_logs, instrument_config_params=None):
div_x = [float(v) for v in list(das_logs.attrs["collimation"].split("-"))]
nxcoll.create_dataset(name="divergence_x", data=div_x, maxshape=None)
nxcoll["divergence_x"].attrs["type"] = "NX_ANGLE"
nxcoll["divergence_x"].attrs["units"] = "minutes of aarc"
nxcoll["divergence_x"].attrs["units"] = "minutes of arc"

except KeyError:
pass
Expand Down
Binary file modified test_data/spice_to_nexus_test_scan34.h5
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