From 8d1719a5834bea141209820a4780d8ecf8795461 Mon Sep 17 00:00:00 2001
From: woutdenolf <woutdenolf@users.sf.net>
Date: Wed, 12 Feb 2025 17:00:16 +0100
Subject: [PATCH] split_bliss_scan: waiting for the end of the scan should be
optional
---
src/est/core/process/split.py | 3 +-
src/est/core/split_monotonic.py | 10 ++++-
src/est/tests/test_split_monotonic.py | 61 +++++++++++++++++++++++++++
3 files changed, 72 insertions(+), 2 deletions(-)
diff --git a/src/est/core/process/split.py b/src/est/core/process/split.py
index dbdd3ce6..1d479773 100644
--- a/src/est/core/process/split.py
+++ b/src/est/core/process/split.py
@@ -6,7 +6,7 @@ from est.core.split_monotonic import split_bliss_scan
class SplitBlissScan(
Task,
input_names=["filename", "scan_number", "monotonic_channel", "out_filename"],
- optional_input_names=["retry_timeout", "retry_period"],
+ optional_input_names=["wait_finished", "retry_timeout", "retry_period"],
output_names=["out_urls"],
):
"""Split a Bliss scan in subscans as determined by a channel which
@@ -21,6 +21,7 @@ class SplitBlissScan(
:param optional_input_names:
+ * ``wait_finished``: Wait for the Bliss scan to be complete in HDF5.
* ``retry_timeout``: Timeout of waiting for the Bliss scan to be complete in HDF5.
* ``retry_period``: Check period of waiting for the Bliss scan to be complete in HDF5.
diff --git a/src/est/core/split_monotonic.py b/src/est/core/split_monotonic.py
index 3c616f75..deab4da6 100644
--- a/src/est/core/split_monotonic.py
+++ b/src/est/core/split_monotonic.py
@@ -18,6 +18,7 @@ def split_bliss_scan(
scan_number: int,
monotonic_channel: str,
out_filename: str,
+ wait_finished: bool = True,
**retry_args,
) -> List[str]:
"""Split a Bliss scan in subscans as determined by a channel which
@@ -27,12 +28,15 @@ def split_bliss_scan(
:param scan_number: The Bliss scan number.
:param monotonic_channel: HDF5 path relative to the scan group.
:param out_filename: HDF5 file name to save subscans as a result of splitting the Bliss scan.
+ :param wait_finished: Wait for the Bliss scan to be complete in HDF5.
:param retry_timeout: Timeout of waiting for the Bliss scan to be complete in HDF5.
:param retry_period: Check period of waiting for the Bliss scan to be complete in HDF5.
:returns: HDF5 URL's of the subscans as a result of splitting the Bliss scan.
"""
entry_name = f"{scan_number}.1"
- _wait_scan_finished(filename, entry_name, **retry_args)
+
+ if wait_finished:
+ _wait_scan_finished(filename, entry_name, **retry_args)
out_urls = []
with h5py_utils.File(filename) as nxroot_in:
@@ -41,6 +45,10 @@ def split_bliss_scan(
monotonic_values = nxentry_in[monotonic_channel][()]
monotonic_slices = split_piecewise_monotonic(monotonic_values)
+ if monotonic_slices and not wait_finished:
+ # The last subscan might not be complete.
+ monotonic_slices = monotonic_slices[:-1]
+
for subscan_number, subscan_slice in enumerate(monotonic_slices, 1):
out_url = _save_subscan(
nxentry_in, scan_number, subscan_number, out_filename, subscan_slice
diff --git a/src/est/tests/test_split_monotonic.py b/src/est/tests/test_split_monotonic.py
index 6cb14b72..a10fc488 100644
--- a/src/est/tests/test_split_monotonic.py
+++ b/src/est/tests/test_split_monotonic.py
@@ -90,6 +90,67 @@ def test_split_bliss_scan(tmp_path, split_function):
assert split_data == expected_split_data
+@pytest.mark.parametrize("split_function", [split_bliss_scan, split_bliss_scan_task])
+def test_split_unfinished_bliss_scan(tmp_path, split_function):
+ bliss_scan_data = {
+ "1.1": {
+ "end_time": "",
+ "@attr1": "value1",
+ "dataset1": "value1",
+ "group1": {
+ "@attr2": 10,
+ "dataset2": "value2",
+ "dataset3": [0, 1, 2, 2, 1, 0],
+ "dataset4": [0, 1, 2, 5, 4, 3],
+ "dataset5": 10,
+ "dataset6": [10, 20],
+ },
+ "group2": {
+ "@attr3": "value3",
+ ">dataset3": "../group1/dataset3",
+ ">dataset4": "/1.1/group1/dataset4",
+ },
+ }
+ }
+
+ expected_split_data = {
+ "1.1": {
+ "@attr1": "value1",
+ "dataset1": "value1",
+ "end_time": "",
+ "group1": {
+ "@attr2": 10,
+ "dataset2": "value2",
+ "dataset3": [0, 1, 2],
+ "dataset4": [0, 1, 2],
+ "dataset5": 10,
+ },
+ "group2": {
+ "@attr3": "value3",
+ "dataset3": [0, 1, 2],
+ "dataset4": [0, 1, 2],
+ },
+ }
+ }
+
+ in_file = str(tmp_path / "in.h5")
+ dictdump.dicttonx(bliss_scan_data, in_file, add_nx_class=False)
+
+ out_file = str(tmp_path / "out.h5")
+ out_urls = split_function(
+ filename=in_file,
+ scan_number=1,
+ monotonic_channel="group1/dataset3",
+ out_filename=out_file,
+ wait_finished=False,
+ )
+
+ assert out_urls == [f"silx://{out_file}::/1.1"]
+
+ split_data = _normalize_h5data(dictdump.nxtodict(out_file, asarray=False))
+ assert split_data == expected_split_data
+
+
@pytest.mark.parametrize("split_function", [split_bliss_scan, split_bliss_scan_task])
def test_split_bliss_scan_timeout(tmp_path, split_function):
bliss_scan_data = {
--
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