def fes_radiograph(raw_source,
radiograph_names=glbl_dict["radiograph_names"],
db=glbl_dict["exp_db"],
resets=None,
**kwargs):
"""Translate from event stream to data for radiograph processing
Parameters
----------
raw_source : Stream
The raw data source
radiograph_names : Stream
The names of the data to perform radiograph transformations on
db : Broker
The databroker with the raw data
resets : list of str
Data keys which when updated with new data cause the averaging to reset
"""
not_dark_scan = FromEventStream(
"start", (), upstream=raw_source, stream_name="not dark scan").map(
lambda x: not x.get("dark_frame", False))
# Fill the raw event stream
source = (
# Emit on works here because we emit on the not_dark_scan first due
# to the ordering of the nodes!
raw_source.combine_latest(
not_dark_scan, emit_on=0).filter(lambda x: x[1]).pluck(0).starmap(
Retrieve(handler_reg=db.reg.handler_reg,
root_map=db.reg.root_map)
).filter(lambda x: x[0] not in ["resource", "datum"]))
# source.sink(lambda x: print('Source says ', x))
# Get all the documents
start_docs = FromEventStream("start", (), source)
descriptor_docs = FromEventStream("descriptor", (),
source,
event_stream_name="primary")
event_docs = FromEventStream("event", (),
source,
event_stream_name="primary")
all_docs = event_docs.combine_latest(
start_docs, descriptor_docs, emit_on=0, first=True).starmap(
lambda e, s, d: {
"raw_event": e,
"raw_start": s,
"raw_descriptor": d,
"human_timestamp": _timestampstr(s["time"]),
})
start_timestamp = FromEventStream("start", ("time", ), source)
if resets:
reset = union(*[
FromEventStream("event", ('data', r), upstream=source).unique(
history=1) for r in resets
])
flat_field_query = start_docs.map(query_flat_field, db=db)
flat_field = union(*[
FromEventStream(
"event",
("data", image_name),
flat_field_query.filter(lambda x: x != []).map(
lambda x: x if not isinstance(x, list) else x[0]).map(
lambda x: x.documents(fill=True)).flatten(),
event_stream_name="primary",
) for image_name in radiograph_names
]).map(np.float32)
# Get foreground dark
fg_dark_query = start_docs.map(query_dark, db=db)
fg_dark_query.filter(lambda x: x == []).sink(
lambda x: print("No dark found!"))
dark = union(*[
FromEventStream(
"event",
("data", image_name),
fg_dark_query.filter(lambda x: x != []).map(
lambda x: x if not isinstance(x, list) else x[0]).map(
lambda x: x.documents(fill=True)).flatten(),
event_stream_name="primary",
) for image_name in radiograph_names
]).map(np.float32)
# Pull darks from their stream if it exists
for image_name in radiograph_names:
(FromEventStream("event", ("data", image_name),
source,
event_stream_name="dark").map(
np.float32).connect(dark))
img = union(*[
FromEventStream(
"event",
("data", image_name),
source,
principle=True,
event_stream_name="primary",
stream_name="raw_foreground",
) for image_name in radiograph_names
]).map(np.float32)
raw_source.starsink(StartStopCallback())
return locals()
def start_gen(
raw_source,
image_names=glbl_dict["image_fields"],
db=glbl_dict["exp_db"],
calibration_md_folder=None,
**kwargs,
):
"""
Parameters
----------
raw_source
image_name
db : databroker.Broker
The databroker to use
calibration_md_folder
kwargs
Returns
-------
"""
if calibration_md_folder is None:
calibration_md_folder = {"folder": "xpdAcq_calib_info.yml"}
# raw_source.sink(lambda x: print(x[0]))
# Build the general pipeline from the raw_pipeline
# TODO: change this when new dark logic comes
# Check that the data isn't a dark (dark_frame = True when taking a dark)
not_dark_scan = FromEventStream(
"start", (), upstream=raw_source, stream_name="not dark scan"
).map(lambda x: not x.get("dark_frame", False))
# Fill the raw event stream
source = (
# Emit on works here because we emit on the not_dark_scan first due
# to the ordering of the nodes!
raw_source.combine_latest(not_dark_scan, emit_on=0)
.filter(lambda x: x[1])
.pluck(0)
.starmap(
Retrieve(handler_reg=db.reg.handler_reg, root_map=db.reg.root_map)
)
.filter(lambda x: x[0] not in ["resource", "datum"])
)
# source.sink(lambda x: print('Source says ', x))
# Get all the documents
start_docs = FromEventStream("start", (), source)
descriptor_docs = FromEventStream(
"descriptor", (), source, event_stream_name="primary"
)
event_docs = FromEventStream(
"event", (), source, event_stream_name="primary"
)
all_docs = event_docs.combine_latest(
start_docs, descriptor_docs, emit_on=0, first=True
).starmap(
lambda e, s, d: {
"raw_event": e,
"raw_start": s,
"raw_descriptor": d,
"human_timestamp": _timestampstr(s["time"]),
}
)
# PDF specific
composition = FromEventStream("start", ("composition_string",), source)
# Calibration information
wavelength = FromEventStream("start", ("bt_wavelength",), source).unique(
history=1
)
calibrant = FromEventStream(
"start", ("dSpacing",), source, principle=True
).unique(history=1)
detector = (
FromEventStream("start", ("detector",), source)
.union(
*[
FromEventStream(
"descriptor",
(
"configuration",
image_name.split("_")[0],
"data",
f'{image_name.split("_")[0]}_detector_type',
),
source,
event_stream_name="primary",
)
for image_name in image_names
]
)
.unique(history=1)
)
is_calibration_img = FromEventStream("start", (), source).map(
lambda x: "detector_calibration_server_uid" in x
)
# Only pass through new calibrations (prevents us from recalculating cals)
geo_input = FromEventStream(
"start", ("calibration_md",), source, principle=True
).unique(history=1)
start_timestamp = FromEventStream("start", ("time",), source)
# Clean out the cached darks and backgrounds on start
# so that this will run regardless of background/dark status
# note that we get the proper data (if it exists downstream)
# FIXME: this is kinda an anti-pattern and needs to go lower in the
# pipeline
start_docs.sink(lambda x: raw_background_dark.emit(0.0))
start_docs.sink(lambda x: raw_background.emit(0.0))
start_docs.sink(lambda x: raw_foreground_dark.emit(0.0))
bg_query = start_docs.map(query_background, db=db)
bg_docs = (
bg_query.zip(start_docs)
.starmap(temporal_prox)
.filter(lambda x: x != [])
.map(lambda x: x[0].documents(fill=True))
.flatten()
)
# Get foreground dark
fg_dark_query = start_docs.map(query_dark, db=db)
fg_dark_query.filter(lambda x: x == []).sink(
lambda x: print("No dark found!")
)
raw_foreground_dark = union(
*[
FromEventStream(
"event",
("data", image_name),
fg_dark_query.filter(lambda x: x != [])
.map(lambda x: x if not isinstance(x, list) else x[0])
.map(lambda x: x.documents(fill=True))
.flatten(),
event_stream_name="primary",
)
for image_name in image_names
]
).map(np.float32)
# Get bg dark
bg_dark_query = FromEventStream("start", (), bg_docs).map(
query_dark, db=db
)
raw_background_dark = union(
*[
FromEventStream(
"event",
("data", image_name),
bg_dark_query.filter(lambda x: x != [])
.map(lambda x: x if not isinstance(x, list) else x[0])
.map(lambda x: x.documents(fill=True))
.flatten(),
stream_name="raw_background_dark",
event_stream_name="primary",
)
for image_name in image_names
]
).map(np.float32)
# Pull darks from their stream if it exists
for image_name in image_names:
(
FromEventStream(
"event", ("data", image_name), source, event_stream_name="dark"
)
.map(np.float32)
.connect(raw_foreground_dark)
)
# Get background
raw_background = union(
*[
FromEventStream(
"event",
("data", image_name),
bg_docs,
stream_name="raw_background",
event_stream_name="primary",
)
for image_name in image_names
]
).map(np.float32)
# Get foreground
img_counter = FromEventStream(
"event",
("seq_num",),
source,
stream_name="seq_num",
# This doesn't make sense in multi-stream settings
event_stream_name="primary",
)
raw_foreground = union(
*[
FromEventStream(
"event",
("data", image_name),
source,
principle=True,
event_stream_name="primary",
stream_name="raw_foreground",
)
for image_name in image_names
]
).map(np.float32)
raw_source.starsink(StartStopCallback())
return locals()
def fes_radiograph(
raw_source,
radiograph_names=glbl_dict["radiograph_names"],
db=glbl_dict["exp_db"],
resets=None,
**kwargs
):
"""Translate from event stream to data for radiograph processing
Parameters
----------
raw_source : Stream
The raw data source
radiograph_names : Stream
The names of the data to perform radiograph transformations on
db : Broker
The databroker with the raw data
resets : list of str
Data keys which when updated with new data cause the averaging to reset
"""
not_dark_scan = FromEventStream(
"start", (), upstream=raw_source, stream_name="not dark scan"
).map(lambda x: not x.get("dark_frame", False))
# Fill the raw event stream
source = (
# Emit on works here because we emit on the not_dark_scan first due
# to the ordering of the nodes!
raw_source.combine_latest(not_dark_scan, emit_on=0)
.filter(lambda x: x[1])
.pluck(0)
.starmap(
Retrieve(handler_reg=db.reg.handler_reg, root_map=db.reg.root_map)
)
.filter(lambda x: x[0] not in ["resource", "datum"])
)
# source.sink(lambda x: print('Source says ', x))
# Get all the documents
start_docs = FromEventStream("start", (), source)
descriptor_docs = FromEventStream(
"descriptor", (), source, event_stream_name="primary"
)
event_docs = FromEventStream(
"event", (), source, event_stream_name="primary"
)
all_docs = event_docs.combine_latest(
start_docs, descriptor_docs, emit_on=0, first=True
).starmap(
lambda e, s, d: {
"raw_event": e,
"raw_start": s,
"raw_descriptor": d,
"human_timestamp": _timestampstr(s["time"]),
}
)
start_timestamp = FromEventStream("start", ("time",), source)
if resets:
reset = union(*[FromEventStream("event", ('data', r), upstream=source).unique(history=1) for r in resets])
flat_field_query = start_docs.map(query_flat_field, db=db)
flat_field = union(
*[
FromEventStream(
"event",
("data", image_name),
flat_field_query.filter(lambda x: x != [])
.map(lambda x: x if not isinstance(x, list) else x[0])
.map(lambda x: x.documents(fill=True))
.flatten(),
event_stream_name="primary",
)
for image_name in radiograph_names
]
).map(np.float32)
# Get foreground dark
fg_dark_query = start_docs.map(query_dark, db=db)
fg_dark_query.filter(lambda x: x == []).sink(
lambda x: print("No dark found!")
)
dark = union(
*[
FromEventStream(
"event",
("data", image_name),
fg_dark_query.filter(lambda x: x != [])
.map(lambda x: x if not isinstance(x, list) else x[0])
.map(lambda x: x.documents(fill=True))
.flatten(),
event_stream_name="primary",
)
for image_name in radiograph_names
]
).map(np.float32)
# Pull darks from their stream if it exists
for image_name in radiograph_names:
(
FromEventStream(
"event", ("data", image_name), source, event_stream_name="dark"
)
.map(np.float32)
.connect(dark)
)
img = union(
*[
FromEventStream(
"event",
("data", image_name),
source,
principle=True,
event_stream_name="primary",
stream_name="raw_foreground",
)
for image_name in radiograph_names
]
).map(np.float32)
raw_source.starsink(StartStopCallback())
return locals()