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Unfinished scan including tests

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This commit is contained in:
steppke_a
2025-11-11 15:09:54 +01:00
parent d397a9668b
commit a70ef5caa2
7 changed files with 1632 additions and 27 deletions
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127
src/cristallina/uscan.py
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@@ -1,47 +1,120 @@
from sfdata import SFScanInfo
import sfdata.utils
import json
import time
from pathlib import Path
from sfdata.utils import print_skip_warning, json_load, adjust_shape
from sfdata.ign import remove_ignored_filetypes_scan
from sfdata import SFDataFiles, SFScanInfo
from partialjson.json_parser import JSONParser
class UnfinishedScan(SFScanInfo):
class UnfinishedScanInfo(SFScanInfo):
"""
Represents an unfinished scan from SwissFEL data, mimicking a finished SFScanInfo. It tries
to parse a partial JSON file and extract the scan information.
Represents an unfinished scan from SwissFEL data, mimicking a finished SFScanInfo. It allows to iterate
over already available scan steps and waits for new data if the scan is still ongoing.
If the scan is already finished, it behaves like a regular SFScanInfo.
Args:
fname (str): The filename of the JSON file to be processed for scan information.
fname (str): The filepath of the JSON file to be processed for scan information (e.g. scan.json).
refresh_interval (int): Time in seconds to wait before checking for new data again. Default is 10 seconds.
"""
def __init__(self, fname):
def __init__(self, fname, refresh_interval=10):
self.fname = fname
self.fs = sfdata.utils.FileStatus(fname)
self.finished = False
self.refresh_interval = refresh_interval
if is_finished_scan(fname):
# simple case, it is a finished scan and our parent can handle it
super().__init__(fname)
self.finished = True
else:
# try to parse it as a partial JSON file
self._parse_partial_json(fname)
def _parse_partial_json(self, fname):
with open(fname) as f:
content = f.read()
parser = JSONParser()
parser = JSONParser()
self.info = info = parser.parse(content)
# we try to extract as much information as possible,
# leaving missing parts out if not available
fnames = info.get("scan_files", [])
self.files = remove_ignored_filetypes_scan(fnames)
self.parameters = info.get("scan_parameters", [])
values = info.get("scan_values", [])
readbacks = info.get("scan_readbacks", [])
# filter for empty values which can occur in the partial json parsing
values = [vals for vals in values if vals]
readbacks = [rb for rb in readbacks if rb]
self.values = adjust_shape(values)
self.readbacks = adjust_shape(readbacks)
self.files = info["scan_files"]
def __iter__(self):
if self.finished:
return super().__iter__()
try:
self.parameters = info["scan_parameters"]
except KeyError:
self.parameters = None
return self._generate_data()
try:
values = info["scan_values"]
values = [v for v in values if v]
except KeyError:
values = None
def _generate_data(self):
"""Generator that yields scan data as it becomes available during the scan."""
yielded_count = 0
while True:
self._parse_partial_json(self.fname)
try:
readbacks = info["scan_readbacks"]
readbacks = [r for r in readbacks if r]
except KeyError:
readbacks = None
# Check if we have new files to yield
while self.files and len(self.files) > yielded_count:
fns = self.files[yielded_count]
if not files_available_on_disk(fns):
time.sleep(self.refresh_interval)
continue # Wait and recheck
self.values = sfdata.utils.adjust_shape(values)
self.readbacks = sfdata.utils.adjust_shape(readbacks)
yielded_count += 1
try:
with SFDataFiles(*fns) as data:
yield data
except Exception as exc:
# TODO: Think about what could go wrong here and deal with it more specifically
sn = f"step {yielded_count - 1} {fns}"
print_skip_warning(exc, sn)
continue # Try next file
if is_finished_scan(self.fname) and (yielded_count >= len(self.files)):
return # Scan is finished, and we yielded all available files, stop iteration
# Wait before checking again
time.sleep(self.refresh_interval)
def is_finished_scan(fname):
""" If the scan.json file is complete, valid and the files are on the disk the scan is finished.
This does not cover the case where a scan is interrupted and continued later.
It also relies on the behavior of RA that the scan.json is only fully written at the end of the scan."""
try:
content = json_load(fname)
files = [file for step in content['scan_files'] for file in step]
# Check if all files are available on disk
if not files_available_on_disk(set(files)):
return False
except json.JSONDecodeError:
return False
return True
def files_available_on_disk(fnames):
"""Check if all files for this step are available on disk and contain some data."""
if all(Path(fn).exists() for fn in fnames):
return all(Path(fn).stat().st_size > 0 for fn in fnames)
return False

108
tests/data/scans/scan1.json Normal file
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@@ -0,0 +1,108 @@
{
"pulseIds": [
[
25378283898,
25378283908
],
[
25378284929,
25378284939
],
[
25378285957,
25378285967
],
[
25378286993,
25378287003
],
[
25378288023,
25378288033
],
[
25378289052,
25378289062
]
],
"scan_files": [
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF20T01V01.h5"
]
],
"scan_parameters": {
"Id": [
"DUMMY"
],
"conversion_factor": [
1
],
"name": [
"Dummy"
],
"offset": [
0
],
"scan_name": "test_slow_acquisition",
"units": [
"au"
]
},
"scan_readbacks": [
[
0.0
],
[
1.0
],
[
2.0
],
[
3.0
],
[
4.0
],
[
5.0
]
],
"scan_readbacks_raw": [
[
0.0
],
[

128
tests/data/scans/scan2.json Normal file
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@@ -0,0 +1,128 @@
{
"pulseIds": [
[
25378283898,
25378283908
],
[
25378284929,
25378284939
],
[
25378285957,
25378285967
],
[
25378286993,
25378287003
],
[
25378288023,
25378288033
],
[
25378289052,
25378289062
],
[
25378290082,
25378290092
]
],
"scan_files": [
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF20T01V01.h5"
]
],
"scan_parameters": {
"Id": [
"DUMMY"
],
"conversion_factor": [
1
],
"name": [
"Dummy"
],
"offset": [
0
],
"scan_name": "test_slow_acquisition",
"units": [
"au"
]
},
"scan_readbacks": [
[
0.0
],
[
1.0
],
[
2.0
],
[
3.0
],
[
4.0
],
[
5.0
],
[
6.0
]
],
"scan_readbacks_raw": [
[
0.0
],
[
1.0
],
[
2.0
],
[

148
tests/data/scans/scan3.json Normal file
View File

@@ -0,0 +1,148 @@
{
"pulseIds": [
[
25378283898,
25378283908
],
[
25378284929,
25378284939
],
[
25378285957,
25378285967
],
[
25378286993,
25378287003
],
[
25378288023,
25378288033
],
[
25378289052,
25378289062
],
[
25378290082,
25378290092
],
[
25378291117,
25378291127
]
],
"scan_files": [
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.JF20T01V01.h5"
]
],
"scan_parameters": {
"Id": [
"DUMMY"
],
"conversion_factor": [
1
],
"name": [
"Dummy"
],
"offset": [
0
],
"scan_name": "test_slow_acquisition",
"units": [
"au"
]
},
"scan_readbacks": [
[
0.0
],
[
1.0
],
[
2.0
],
[
3.0
],
[
4.0
],
[
5.0
],
[
6.0
],
[
7.0
]
],
"scan_readbacks_raw": [
[
0.0
],
[
1.0
],
[
2.0
],
[
3.0
],
[
4.0
],
[
5.0

328
tests/data/scans/scan4.json Normal file
View File

@@ -0,0 +1,328 @@
{
"pulseIds": [
[
25378283898,
25378283908
],
[
25378284929,
25378284939
],
[
25378285957,
25378285967
],
[
25378286993,
25378287003
],
[
25378288023,
25378288033
],
[
25378289052,
25378289062
],
[
25378290082,
25378290092
],
[
25378291117,
25378291127
],
[
25378292146,
25378292156
],
[
25378293176,
25378293186
],
[
25378294206,
25378294216
],
[
25378295236,
25378295246
],
[
25378296272,
25378296282
],
[
25378297301,
25378297311
],
[
25378298330,
25378298340
],
[
25378299359,
25378299369
],
[
25378300389,
25378300399
]
],
"scan_files": [
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0001.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0002.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0003.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0004.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0005.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0006.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0007.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0008.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0009.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0009.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0009.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0009.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0010.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0010.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0010.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0010.JF20T01V01.h5"
],
[
"/sf/cristallina/data/p19150/raw/run0531/data/acq0011.PVDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0011.BSDATA.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0011.JF16T03V02.h5",
"/sf/cristallina/data/p19150/raw/run0531/data/acq0011.JF20T01V01.h5"
],
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