From dd59d29ff701c25ac977e2f81af8a9a939ccadf7 Mon Sep 17 00:00:00 2001
From: Samuel Jackson <samueljackson@outlook.com>
Date: Mon, 28 Jan 2019 15:23:40 +0000
Subject: [PATCH] Add support for Jana format with modulated peaks
---
.../plugins/algorithms/SaveReflections.py | 45 ++++++++-----------
.../plugins/algorithms/SaveReflectionsTest.py | 6 ++-
.../UnitTest/jana_format_modulated.hkl.md5 | 1 +
docs/source/release/v3.14.0/diffraction.rst | 1 +
4 files changed, 25 insertions(+), 28 deletions(-)
create mode 100644 Testing/Data/UnitTest/jana_format_modulated.hkl.md5
diff --git a/Framework/PythonInterface/plugins/algorithms/SaveReflections.py b/Framework/PythonInterface/plugins/algorithms/SaveReflections.py
index d2b28cb2661..265743f523c 100644
--- a/Framework/PythonInterface/plugins/algorithms/SaveReflections.py
+++ b/Framework/PythonInterface/plugins/algorithms/SaveReflections.py
@@ -6,7 +6,7 @@
# SPDX - License - Identifier: GPL - 3.0 +
import re
import numpy as np
-from mantid.api import AlgorithmFactory, FileProperty, FileAction, PythonAlgorithm, ITableWorkspaceProperty
+from mantid.api import AlgorithmFactory, FileProperty, FileAction, PythonAlgorithm, ITableWorkspaceProperty, IPeaksWorkspace
from mantid.kernel import StringListValidator, Direction
from mantid.simpleapi import SaveHKL
@@ -168,9 +168,6 @@ class JanaFormat(object):
:param file_name: the file name to output data to.
:param workspace: the PeaksWorkspace to write to file.
"""
- if has_modulated_indexing(workspace):
- raise NotImplementedError("Cannot currently save modulated structures to Jana format")
- self._cache_instrument_params(workspace)
with open(file_name, 'w') as f_handle:
self.write_header(f_handle, workspace)
self.write_peaks(f_handle, workspace)
@@ -181,11 +178,13 @@ class JanaFormat(object):
:param f_handle: handle to the file to write to.
:param workspace: the PeaksWorkspace to save to file.
"""
- sample = workspace.sample()
- lattice = sample.getOrientedLattice()
- lattice_params = [lattice.a(), lattice.b(), lattice.c(), lattice.alpha(), lattice.beta(), lattice.gamma()]
- lattice_params = "".join(["{: >10.4f}".format(value) for value in lattice_params])
- f_handle.write("# Lattice parameters {}\n".format(lattice_params))
+ if isinstance(workspace, IPeaksWorkspace):
+ sample = workspace.sample()
+ lattice = sample.getOrientedLattice()
+ lattice_params = [lattice.a(), lattice.b(), lattice.c(), lattice.alpha(), lattice.beta(), lattice.gamma()]
+ lattice_params = "".join(["{: >10.4f}".format(value) for value in lattice_params])
+ f_handle.write("# Lattice parameters {}\n".format(lattice_params))
+
f_handle.write("(3i5,2f12.2,i5,4f10.4)\n")
def write_peaks(self, f_handle, workspace):
@@ -219,29 +218,21 @@ class JanaFormat(object):
f_handle.write("{SigInt: >12.2f}".format(**peak))
f_handle.write("{: >5.0f}".format(1))
f_handle.write("{Wavelength: >10.4f}".format(**peak))
- f_handle.write("{: >10.4f}".format(self._get_two_theta(peak['DetID'])))
+ f_handle.write("{: >10.4f}".format(self._get_two_theta(peak)))
f_handle.write("{: >10.4f}{: >10.4f}{: >10.4f}".format(1.0, 0.0, 0.0))
f_handle.write("\n")
- def _get_two_theta(self, det_id):
- """Get the two theta value for this peak
- :param det_id: the detector ID of this Peak
- """
- det = self._instrument.getDetector(det_id)
- return np.degrees(det.getTwoTheta(self._instrument.getPos(), self._z_axis))
-
- def _cache_instrument_params(self, workspace):
- """Cache some parameters about the instrument
-
- This stores some of the instrument parameters at the start
- of execution so we can quickly access them later.
+ def _get_two_theta(self, peak):
+ """Get the two theta value for this peak.
- :param workspace: the PeaksWorkspace to cache instrument data from.
+ This is just Bragg's law relating wavelength to scattering angle.
+ :param peak: peak object to get the scattering angle for.
+ :returns: the scattering angle for the peak.
"""
- self._instrument = workspace.getInstrument()
- frame = self._instrument.getReferenceFrame()
- self._z_axis = frame.vecPointingAlongBeam()
-
+ d = peak['DSpacing']
+ wavelength = peak['Wavelength']
+ theta = 2.*np.arcsin(0.5*(wavelength / d))
+ return np.rad2deg(theta)
# ------------------------------------------------------------------------------------------------------
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/SaveReflectionsTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/SaveReflectionsTest.py
index 63af0dd771b..403019976a8 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/SaveReflectionsTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/SaveReflectionsTest.py
@@ -140,11 +140,15 @@ class SaveReflectionsTest(unittest.TestCase):
def test_save_jana_format_modulated(self):
# Arrange
workspace = self._create_modulated_peak_table()
+ reference_result = self._get_reference_result("jana_format_modulated.hkl")
file_name = os.path.join(self._test_dir, "test_jana_modulated.hkl")
output_format = "Jana"
# Act
- self.assertRaises(RuntimeError, SaveReflections, InputWorkspace=workspace, Filename=file_name, Format=output_format)
+ SaveReflections(InputWorkspace=workspace, Filename=file_name, Format=output_format)
+
+ # Assert
+ self.assertTrue(compare_file(reference_result, file_name))
def test_save_GSAS_format(self):
# Arrange
diff --git a/Testing/Data/UnitTest/jana_format_modulated.hkl.md5 b/Testing/Data/UnitTest/jana_format_modulated.hkl.md5
new file mode 100644
index 00000000000..148d77dbf3f
--- /dev/null
+++ b/Testing/Data/UnitTest/jana_format_modulated.hkl.md5
@@ -0,0 +1 @@
+96c8aa0e0a91f2c537ec06f0170d7d25
diff --git a/docs/source/release/v3.14.0/diffraction.rst b/docs/source/release/v3.14.0/diffraction.rst
index 30df5d2faae..6e3734d6d24 100644
--- a/docs/source/release/v3.14.0/diffraction.rst
+++ b/docs/source/release/v3.14.0/diffraction.rst
@@ -77,6 +77,7 @@ Improvements
- Focus on Pearl now saves out xye_tof files.
- :ref:`PDLoadCharacterizations <algm-PDLoadCharacterizations>` now sets the same run numbers for all rows when using an ``exp.ini`` file.
- Focus now checks if the vanadium for a run is already loaded before loading it in to prevent reloading the same vanadium multiple times.
+- :ref:`SaveReflections <algm-SaveReflections>` now supports saving indexed modulated peaks in the Jana format.
Bugfixes
--
GitLab