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export_tools.py
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import datetime
import numpy as np
from os.path import join
from tiled.client import from_uri
from autoprocess.statelessAnalysis import get_tes_data
from autoprocess.utils import run_is_processed
import re
def initialize_tiled_client(beamline_acronym):
return from_uri("https://tiled.nsls2.bnl.gov")[beamline_acronym]["raw"]
def get_proposal_path(run):
proposal = run.start.get("proposal", {}).get("proposal_id", None)
is_commissioning = "commissioning" in run.start.get("proposal", {}).get("type", "").lower()
cycle = run.start.get("cycle", None)
if proposal is None or cycle is None:
raise ValueError("Proposal Metadata not Loaded")
if is_commissioning:
proposal_path = f"/nsls2/data/sst/proposals/commissioning/pass-{proposal}/"
else:
proposal_path = f"/nsls2/data/sst/proposals/{cycle}/pass-{proposal}/"
return proposal_path
def get_with_fallbacks(thing, *possible_names, default=None):
for name in possible_names:
if isinstance(name, (list, tuple)):
for subname in name:
if subname in thing:
thing = thing[subname]
found_thing = True
else:
found_thing = False
if found_thing:
return thing
elif name in thing:
return thing[name]
return default
def get_header_and_data(run):
cols, run_data, rois = get_run_data(run)
header = get_run_header(run)
header["channelinfo"]["cols"] = cols
data = np.vstack(run_data).T
return header, data
def get_run_header(run):
metadata = {}
scaninfo = {}
scaninfo["scan"] = run.start["scan_id"]
scaninfo["date"] = datetime.datetime.fromtimestamp(run.start["time"]).isoformat()
scaninfo["sample"] = run.start.get("sample_name", "")
scaninfo["loadid"] = run.start.get("sample_id", "")
scaninfo["command"] = get_with_fallbacks(run.start, "command", "plan_name", default=None)
scaninfo["motor"] = run.start.get("motors", ["time"])[0]
scankeys = [
"time",
"data_session",
"cycle",
"start_datetime",
"repeat",
]
for k in scankeys:
if k in run.start:
scaninfo[k] = run.start[k]
if "ref_args" in run.start:
scaninfo["ref_edge"] = run.start["ref_args"]["i0up_multimesh_sample_sample_name"]["value"]
scaninfo["ref_id"] = run.start["ref_args"]["i0up_multimesh_sample_sample_id"]["value"]
scaninfo["uid"] = run.start["uid"]
motors = {}
baseline = run.baseline.data.read()
motors["exslit"] = get_with_fallbacks(baseline, "eslit", "Exit Slit of Mono Vertical Gap")[0].item()
motors["manipx"] = float(get_with_fallbacks(baseline, "manip_x", "Manipulator_x", default=[0])[0])
motors["manipy"] = float(get_with_fallbacks(baseline, "manip_y", "Manipulator_y", default=[0])[0])
motors["manipz"] = float(get_with_fallbacks(baseline, "manip_z", "Manipulator_z", default=[0])[0])
motors["manipr"] = float(get_with_fallbacks(baseline, "manip_r", "Manipulator_r", default=[0])[0])
motors["samplex"] = float(get_with_fallbacks(baseline, "manip_sx", "Manipulator_sx", default=[0])[0])
motors["sampley"] = float(get_with_fallbacks(baseline, "manip_sy", "Manipulator_sy", default=[0])[0])
motors["samplez"] = float(get_with_fallbacks(baseline, "manip_sz", "Manipulator_sz", default=[0])[0])
motors["sampler"] = float(get_with_fallbacks(baseline, "manip_sr", "Manipulator_sr", default=[0])[0])
motors["tesz"] = float(get_with_fallbacks(baseline, "tesz", default=[0])[0])
metadata["scaninfo"] = scaninfo
metadata["motors"] = motors
metadata["channelinfo"] = {}
return metadata
def get_run_data(run, omit=[]):
first_keys = [
"en_energy_setpoint",
"en_energy",
"nexafs_i0up",
"nexafs_i1",
"nexafs_ref",
"nexafs_sc",
"nexafs_pey",
]
last_keys = [
"time",
"seconds",
]
config = run.primary.descriptors[0]["configuration"]
exposure = get_with_fallbacks(
config,
["nexafs_i0up", "data", "nexafs_i0up_exposure_time"],
["nexafs_i1", "data", "nexafs_i0up_exposure_time"],
["nexafs_sc", "data", "ucal_sc_exposure_time"],
)
if exposure is None:
exposure = 0
exposure = float(exposure)
columns = []
datadict = {}
known_array_keys = ["tes_mca_spectrum", "spectrum"]
keys = run.primary.data.keys()
usekeys = []
for key in keys:
if key in known_array_keys:
continue
usekeys.append(key)
data = run.primary.data.read(usekeys)
# Add a try-except here after testing
save_directory = join(get_proposal_path(run), "ucal_processing")
if run_is_processed(run, save_directory):
rois, tes_data = get_tes_data(run, save_directory)
else:
print(f"No TES Data is Processed for {run.start['scan_id']}")
rois = {}
tes_data = {}
for key in rois:
if key not in usekeys:
usekeys.append(key)
for key in usekeys:
if key in tes_data:
if len(tes_data[key].shape) == 1:
datadict[key] = tes_data[key]
else:
if len(data[key].shape) == 1:
datadict[key] = data[key].data
if "seconds" not in datadict:
datadict["seconds"] = np.zeros_like(datadict[key]) + exposure
for k in first_keys:
if k in datadict.keys() and k not in omit:
columns.append(k)
for k in datadict.keys():
if k not in columns and k not in omit and k not in last_keys:
columns.append(k)
for k in last_keys:
if k in datadict.keys() and k not in omit:
columns.append(k)
data = [datadict[k] for k in columns]
return columns, data, rois
def add_comment_to_lines(multiline_string, comment_char="#"):
"""
Adds a comment character to the beginning of each line in a multiline string.
Parameters
----------
multiline_string : str
The input multiline string.
Returns
-------
str
The multiline string with comment characters added to each line.
"""
commented_lines = [f"{comment_char} " + line for line in multiline_string.split("\n")]
return "\n".join(commented_lines)
def sanitize_filename(filename):
"""
Sanitize a filename by removing/replacing invalid characters. Avoids wrecking
either Windows or Linux paths.
Eliminates any characters that aren't alphanumeric, period, hyphen, underscore, forward slash, colon, or backslash
Replaces multiple hyphens with a single hyphen
Replaces whitespace and multiple underscores with a single underscore
Parameters
----------
filename : str
The filename to sanitize
Returns
-------
str
The sanitized filename with invalid characters removed/replaced
"""
# Replace any characters that aren't alphanumeric, period, hyphen, underscore, forward slash, colon, or backslash
filename = re.sub(r"[^\w\s\-\./:\\]", "", filename)
# Replace multiple hyphens with single hyphen
filename = re.sub(r"-+", "-", filename)
# Replace whitespace and multiple underscores with single underscore
filename = re.sub(r"[_\s]+", "_", filename)
return filename