From e06ba6842a57b9b12e5044807a97b0ad432f34f1 Mon Sep 17 00:00:00 2001
From: Danilo Ferreira de Lima <danilo.enoque.ferreira.de.lima@xfel.de>
Date: Tue, 5 Sep 2023 14:16:06 +0200
Subject: [PATCH] Avoid setting NDARRAY properties: they cannot be serialized
in JSON.
---
src/calng/CrystfelRunner.py | 43 ++++++++++++++++++++++++++++++++-----
1 file changed, 38 insertions(+), 5 deletions(-)
diff --git a/src/calng/CrystfelRunner.py b/src/calng/CrystfelRunner.py
index e370a055..937ad889 100644
--- a/src/calng/CrystfelRunner.py
+++ b/src/calng/CrystfelRunner.py
@@ -329,8 +329,33 @@ class CrystfelRunner(PythonDevice):
.initialValue([0.0, 0.0])
.commit(),
- NDARRAY_ELEMENT(expected)
- .key("crystfelStats.cell")
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_a")
+ .readOnly()
+ .commit(),
+
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_b")
+ .readOnly()
+ .commit(),
+
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_c")
+ .readOnly()
+ .commit(),
+
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_alpha")
+ .readOnly()
+ .commit(),
+
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_beta")
+ .readOnly()
+ .commit(),
+
+ VECTOR_FLOAT_ELEMENT(expected)
+ .key("crystfelStats.cell_gamma")
.readOnly()
.commit(),
)
@@ -806,9 +831,17 @@ class CrystfelRunner(PythonDevice):
self._results['reflections'] = (sum(n_reflections)
if len(n_reflections) > 0
else 0)
- self._results['cell'] = (np.stack(cell, axis=0)
- if len(cell) > 0
- else np.empty((0, 6), dtype=np.float32))
+ cell_stacked = (np.stack(cell, axis=0)
+ if len(cell) > 0
+ else list())
+ if len(cell_stacked) == 0:
+ for k in ['cell_a', 'cell_b', 'cell_c',
+ 'cell_alpha', 'cell_beta', 'cell_gamma']:
+ self._results[k] = list()
+ else:
+ for i, k in enumerate(['cell_a', 'cell_b', 'cell_c',
+ 'cell_alpha', 'cell_beta', 'cell_gamma']):
+ self._results[k] = cell_stacked[:, i].tolist()
self._results['all_det_centre'] = (np.stack(det_centre, axis=0)
if len(det_centre) > 0
else np.empty((0, 2), dtype=np.float32))
--
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