Skip to content

Commit

Permalink
MNT #81 ready for beamline testing
Browse files Browse the repository at this point in the history
  • Loading branch information
@prjemian
prjemian committed Oct 16, 2024
1 parent 63c78ba commit 0342e8f
Showing 1 changed file with 115 additions and 97 deletions.
212 changes: 115 additions & 97 deletions src/instrument/plans/mesh_plans.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,41 +4,7 @@
.. automodule::
~mesh_list_grid_scan
~xpcs_mesh
..
usage: boost_corr [-h] -r RAW_FILENAME -q QMAP_FILENAME [-o OUTPUT_DIR] [-s SMOOTH] [-i GPU_ID] [-begin_frame BEGIN_FRAME] [-end_frame END_FRAME] [-stride_frame STRIDE_FRAME]
[-avg_frame AVG_FRAME] [-t TYPE] [-dq TYPE] [--verbose] [--dryrun] [--overwrite] [-c CONFIG.JSON]
Compute Multi-tau/Twotime correlation for XPCS datasets on GPU/CPU
optional arguments:
-h, --help show this help message and exit
-r RAW_FILENAME, --raw RAW_FILENAME
the filename of the raw data file (imm/rigaku/hdf)
-q QMAP_FILENAME, --qmap QMAP_FILENAME
the filename of the qmap file (h5/hdf)
-o OUTPUT_DIR, --output OUTPUT_DIR
[default: cluster_results] the output directory for the result file. If not exit, the program will create this directory.
-s SMOOTH, --smooth SMOOTH
[default: sqmap] smooth method to be used in Twotime correlation.
-i GPU_ID, --gpu_id GPU_ID
[default: -1] choose which GPU to use. if the input is -1, then CPU is used
-begin_frame BEGIN_FRAME
[default: 1] begin_frame specifies which frame to begin with for the correlation. This is useful to get rid of the bad frames in the beginning.
-end_frame END_FRAME [default: -1] end_frame specifies the last frame used for the correlation. This is useful to get rid of the bad frames in the end. If -1 is used, end_frame will be set to
the number of frames, i.e. the last frame
-stride_frame STRIDE_FRAME
[default: 1] stride_frame defines the stride.
-avg_frame AVG_FRAME [default: 1] stride_frame defines the number of frames to be averaged before the correlation.
-t TYPE, --type TYPE [default: "Multitau"] Analysis type: ["Multitau", "Twotime", "Both"].
-dq TYPE, --dq_selection TYPE
[default: "all"] dq_selection: a string that select the dq list, eg. '1, 2, 5-7' selects [1,2,5,6,7]. If 'all', all dynamic qindex will be used.
--verbose, -v verbose
--dryrun, -dr dryrun: only show the argument without execution.
--overwrite, -ow whether to overwrite the existing result file.
-c CONFIG.JSON, --config CONFIG.JSON
configuration file to be used. if the same key is passed as an argument, the value in the configure file will be omitted.
~xpcs_mesh_with_dm
"""

import datetime
Expand Down Expand Up @@ -101,11 +67,10 @@ def mesh_list_grid_scan(
"""
Scan over a multi-dimensional mesh.
Collect a total of $n$ points; each motor is on an independent trajectory.
Collect a total of 'n' points; each motor has its own set of positions.
Here, the motors are specified as motor **names** (to match the queueserver
interface). With the names, the ophyd registry is searched for the actual
motor object.
Motors are specified by their **names** (matching the queueserver
interface). The ophyd registry is searched by name for the motor object.
Calls: ``apstools.plans.xpcs_mesh.mesh_list_grid_scan()``. See that plan
for a detailed description of its arguments.
Expand All @@ -132,11 +97,6 @@ def mesh_list_grid_scan(
return uid


def position_list(start, end, numPts):
"""Return a list of positions from start to end with numPts points."""
return np.linspace(start, end, numPts).tolist()


def validate_xpcs_mesh_inputs(
area_det_name,
data_path,
Expand Down Expand Up @@ -195,11 +155,7 @@ def wait_daq_image_file_upload(


def xpcs_mesh(
title=SUGGESTION["title"], # used as part of file name
description=SUGGESTION["description"],
header: str = xpcs_dm.header.get(),
# ---- parameters for data acquisition
area_det_name=SUGGESTION["area_det_name"],
area_det_name="eiger4M",
detectors=None,
m1="sample.x",
s1=0,
Expand All @@ -215,14 +171,7 @@ def xpcs_mesh(
acquire_period=0.001,
nframes=1_000,
# header_index="A001",
# ---- parameters for analysis code (in DM workflow)
# see https://github.com/azjk/boost_corr?tab=readme-ov-file#usage
qmap_file=SUGGESTION["QMAP_file"],
smooth=SUGGESTION["smooth"],
analysisMachine=SUGGESTION["analysisMachine"],
# FIXME:
# ----
md: dict = None,
md=None,
):
"""
Measure XPCS in repeated passes through a 2-D mesh as a single bluesky run.
Expand All @@ -245,7 +194,83 @@ def xpcs_mesh(
At each collection, the area detector will acquire 'nframes' with
acquisition parameters 'acquire_time' & 'acquire_period'.
"""
# 'title' must be safe to use as a file name (no spaces or special chars)
# Only used for XPCS data collection
# Area detector is configured different for each of these.

if detectors is None:
detectors = []
m1_positions = np.linspace(s1, e1, n1).tolist()
m2_positions = np.linspace(s2, e2, n2).tolist()

area_det = oregistry.find(area_det_name)
if area_det in detectors:
# fmt: off
yield from bps.mv(
area_det.cam.acquire_time, acquire_time,
area_det.cam.acquire_period, acquire_period,
area_det.cam.num_images, nframes,
)
# fmt: on
# TODO: add user control of detector trigger_mode
# Includes configuration of soft glue as needed.
# Probably will need more user keywords for this.

yield from mesh_list_grid_scan(
[area_det] + detectors,
m1,
m1_positions,
m2,
m2_positions,
number_of_collection_points=number_of_collection_points,
snake_axes=snake_axes,
md=None,
)


def xpcs_mesh_with_dm(
title=SUGGESTION["title"], # used as part of file name
description=SUGGESTION["description"],
header: str = xpcs_dm.header.get(),
# ---- parameters for data acquisition
area_det_name=SUGGESTION["area_det_name"],
detectors=None,
m1="sample.x",
s1=0,
e1=1,
n1=3,
m2="sample.y",
s2=0,
e2=2,
n2=5,
number_of_collection_points=20,
snake_axes=False,
acquire_time=0.001,
acquire_period=0.001,
nframes=1_000,
# header_index="A001",
# ---- parameters for analysis code (in DM workflow)
# see https://github.com/azjk/boost_corr?tab=readme-ov-file#usage
analysisMachine=SUGGESTION["analysisMachine"],
qmap_file=SUGGESTION["QMAP_file"],
wf_smooth=SUGGESTION["smooth"],
wf_gpuID=-1,
wf_beginFrame=1,
wf_endFrame=-1,
wf_strideFrame=1,
wf_avgFrame=1,
wf_type="Multitau",
wf_dq="all",
wf_verbose=False,
wf_saveG2=False,
wf_overwrite=False,
# ----
md: dict = None,
):
"""
Plan: acquire with xpcs_mesh() then execute DM workflow.
"""
############################################################
#! 'title' must be safe to use as a file name (no spaces or special chars)
safe_title = cleanupText(title)
data_path = pathlib.Path(
xpcs_dm.data_path(
Expand All @@ -255,7 +280,7 @@ def xpcs_mesh(
)

############################################################
# Fail early, fail hard! Check inputs before configuration.
#! Check inputs before configuration. Fail early, fail hard!

validate_xpcs_mesh_inputs(
area_det_name,
Expand All @@ -265,28 +290,15 @@ def xpcs_mesh(
)

############################################################
# Area detector is configured different for each of these.
#! Area detector.

if detectors is None:
detectors = []
m1_positions = position_list(s1, e1, n1)
m2_positions = position_list(s2, e2, n2)

area_det = oregistry.find(area_det_name)
if area_det in detectors:
# fmt: off
yield from bps.mv(
area_det.cam.acquire_time, acquire_time,
area_det.cam.acquire_period, acquire_period,
area_det.cam.num_images, nframes,
)
# fmt: on
# TODO: add user control of detector trigger_mode
# Includes configuration of soft glue as needed.
# Probably will need more user keywords for this.

############################################################
# DM parameters
#! DM parameters

dm_experiment_object = dm_api_ds().getExperimentByName(
xpcs_dm.experiment_name.get()
Expand All @@ -295,7 +307,7 @@ def xpcs_mesh(
logger.info("DM experiment: %s", xpcs_dm.experiment_name.get())

############################################################
# Organize metadata: BS, DM
#! Organize metadata: BS, DM

md_bs = dict( # bluesky plan metadata dict
area_det_name=area_det_name,
Expand All @@ -313,21 +325,31 @@ def xpcs_mesh(
acquire_time=acquire_time,
acquire_period=acquire_period,
nframes=nframes,
# md about the DM
analysisMachine=analysisMachine,
# md about the DM but not in md_dm
workflow_name=workflow_name,
experiment_name=xpcs_dm.experiment_name.get(),
)
md_dm = dict(
md_dm = dict( # will be passed verbatim to DM workflow, as **md_dm
analysisMachine=analysisMachine,
avgFrame=wf_avgFrame,
beginFrame=wf_beginFrame,
dq=wf_dq,
endFrame=wf_endFrame,
gpuID=wf_gpuID,
overwrite=wf_overwrite,
qmap_file=qmap_file,
smooth=smooth,
# FIXME:
saveG2=wf_saveG2,
smooth=wf_smooth,
strideFrame=wf_strideFrame,
type=wf_type,
verbose=wf_verbose,
)

############################################################
# Setup area detector HDF5 plugin (with data_path)
#! Setup area detector HDF5 plugin (with data_path)

master_file_base = xpcs_dm.filename_base(
# no path, no extension
safe_title,
number_of_collection_points,
)
Expand All @@ -339,7 +361,7 @@ def xpcs_mesh(
)

############################################################
# DM DAQ upload the QMAP file to @voyager
#! DM DAQ upload the QMAP file to @voyager

qmap_path = pathlib.Path(qmap_file)
daqInfo_qmap_upload = dm_api_daq().upload(
Expand All @@ -350,15 +372,15 @@ def xpcs_mesh(
logger.info("DM DAQ upload id: %r", daqInfo_qmap_upload["id"])

############################################################
# NeXus master file
#! NeXus master file

hdf5_master_file = master_file_base + MASTER_EXTENSION
nxwriter.warn_on_missing_content = False
nxwriter.file_path = data_path
nxwriter.file_name = data_path / hdf5_master_file

############################################################
# Data Acquisition: run the bluesky plan, wait for the files
#! Data Acquisition: run the bluesky plan, wait for the files

dm_workflow = DM_WorkflowConnector(name="dm_workflow")

Expand All @@ -378,22 +400,21 @@ def acquire():
"title": title,
"description": description,
"datetime": str(datetime.datetime.now()),
"catalog": cat.name,
}
md_xpcs_mesh.update(md_bs)
md_xpcs_mesh["data_management"] = md_dm
md_xpcs_mesh.update(md) # user md takes highest priority

uid = yield from mesh_list_grid_scan(
# fmt: off
uid = yield from xpcs_mesh(
[area_det] + detectors,
m1,
m1_positions,
m2,
m2_positions,
m1, s1, e1, n1,
m2, s2, e2, n2,
number_of_collection_points=number_of_collection_points,
snake_axes=snake_axes,
md=md_xpcs_mesh,
)
# fmt: on
return uid

uid = yield from acquire()
Expand All @@ -407,7 +428,7 @@ def acquire():
yield from wait_daq_image_file_upload(dm_experiment_object, ad_file)

############################################################
# Start DM workflow (optional: and wait for it to finish)
#! Start DM workflow (optional: and wait for it to finish)

logger.info(
"DM workflow %r, filePath=%r",
Expand All @@ -422,14 +443,11 @@ def acquire():
filePath=pathlib.Path(ad_file).name,
experimentName=xpcs_dm.experiment_name.get(),
qmap=qmap_path.name,
# from the plan's API
smooth=smooth,
# FIXME:
analysisMachine=analysisMachine,
**md_dm, # all other kwargs
)

############################################################
# Upload bluesky run metadata to APS DM
#! Upload bluesky run metadata to APS DM

share_bluesky_metadata_with_dm(
xpcs_dm.experiment_name.get(),
Expand All @@ -438,6 +456,6 @@ def acquire():
)

############################################################
# complete
#! complete

logger.info("Finished: xpcs_mesh()")

0 comments on commit 0342e8f

Please sign in to comment.