From 206ad5b41fd17ddd8540cdb77f8911cfb23fd250 Mon Sep 17 00:00:00 2001
From: payno <henri.payno@gmail.com>
Date: Fri, 13 Dec 2024 14:58:27 +0100
Subject: [PATCH] NXtomoeditor: add handling of source / sample distance
Rename some 'distance' to smaple- detector distance
---
src/tomwer/gui/edit/nxtomoeditor.py | 82 ++++++++++++++-----
src/tomwer/gui/edit/tests/test_nx_editor.py | 35 ++++++--
.../test/test_nx_tomo_metadata_viewer.py | 4 +-
src/tomwer/tasks/edit/nxtomoeditor.py | 15 ++++
.../widgets/edit/tests/test_nxtomo_editor.py | 5 +-
5 files changed, 110 insertions(+), 31 deletions(-)
diff --git a/src/tomwer/gui/edit/nxtomoeditor.py b/src/tomwer/gui/edit/nxtomoeditor.py
index dc1a338009..d5e4fce156 100644
--- a/src/tomwer/gui/edit/nxtomoeditor.py
+++ b/src/tomwer/gui/edit/nxtomoeditor.py
@@ -114,8 +114,26 @@ class NXtomoEditor(qt.QWidget):
self._energyLockerLB.setMaximumSize(30, 30)
self._lockerPBs.append(self._energyLockerLB)
self._tree.setItemWidget(self._energyQTWI, 2, self._energyLockerLB)
+ # 1.1 source
+ self._sourceQTWI = qt.QTreeWidgetItem(self._instrumentQTWI)
+ self._sourceQTWI.setText(0, "source")
+ self._sourceSampleDistanceQTWI = qt.QTreeWidgetItem(self._sourceQTWI)
+ self._sourceSampleDistanceQTWI.setText(0, "distance")
+
+ self._sourceSampleDistanceMetricEntry = MetricEntry("", parent=self)
+ self._sourceSampleDistanceMetricEntry.layout().setContentsMargins(2, 2, 2, 2)
+ self._tree.setItemWidget(
+ self._sourceSampleDistanceQTWI, 1, self._sourceSampleDistanceMetricEntry
+ )
+ self._editableWidgets.append(self._sourceSampleDistanceMetricEntry)
+ self._sourceSampleDistanceLB = PadlockButton(self)
+ self._sourceSampleDistanceLB.setMaximumSize(30, 30)
+ self._lockerPBs.append(self._sourceSampleDistanceLB)
+ self._tree.setItemWidget(
+ self._sourceSampleDistanceQTWI, 2, self._sourceSampleDistanceLB
+ )
- # 1.1 detector
+ # 1.2 detector
self._detectorQTWI = qt.QTreeWidgetItem(self._instrumentQTWI)
self._detectorQTWI.setText(0, "detector")
## pixel size
@@ -141,19 +159,21 @@ class NXtomoEditor(qt.QWidget):
self._lockerPBs.append(self._yPixelSizeLB)
self._tree.setItemWidget(self._yPixelSizeQTWI, 2, self._yPixelSizeLB)
- ## distance
+ ## sample - detector distance
self._sampleDetectorDistanceQTWI = qt.QTreeWidgetItem(self._detectorQTWI)
self._sampleDetectorDistanceQTWI.setText(0, "distance")
- self._distanceMetricEntry = MetricEntry("", parent=self)
- self._distanceMetricEntry.layout().setContentsMargins(2, 2, 2, 2)
+ self._sampleDetectorDistanceMetricEntry = MetricEntry("", parent=self)
+ self._sampleDetectorDistanceMetricEntry.layout().setContentsMargins(2, 2, 2, 2)
+ self._tree.setItemWidget(
+ self._sampleDetectorDistanceQTWI, 1, self._sampleDetectorDistanceMetricEntry
+ )
+ self._editableWidgets.append(self._sampleDetectorDistanceMetricEntry)
+ self._sampleDetectorDistanceLB = PadlockButton(self)
+ self._sampleDetectorDistanceLB.setMaximumSize(30, 30)
+ self._lockerPBs.append(self._sampleDetectorDistanceLB)
self._tree.setItemWidget(
- self._sampleDetectorDistanceQTWI, 1, self._distanceMetricEntry
+ self._sampleDetectorDistanceQTWI, 2, self._sampleDetectorDistanceLB
)
- self._editableWidgets.append(self._distanceMetricEntry)
- self._distanceLB = PadlockButton(self)
- self._distanceLB.setMaximumSize(30, 30)
- self._lockerPBs.append(self._distanceLB)
- self._tree.setItemWidget(self._sampleDetectorDistanceQTWI, 2, self._distanceLB)
## field of view
self._fieldOfViewQTWI = qt.QTreeWidgetItem(self._detectorQTWI)
@@ -210,6 +230,7 @@ class NXtomoEditor(qt.QWidget):
self._sampleQTWI.setExpanded(True)
self._beamQTWI.setExpanded(True)
self._detectorQTWI.setExpanded(True)
+ self._sourceQTWI.setExpanded(True)
self.hideLockers(hide_lockers)
# connect signal / slot
@@ -219,8 +240,14 @@ class NXtomoEditor(qt.QWidget):
self._xPixelSizeLB.toggled.connect(self._editingFinished)
self._yPixelSizeMetricEntry.editingFinished.connect(self._editingFinished)
self._yPixelSizeLB.toggled.connect(self._editingFinished)
- self._distanceMetricEntry.editingFinished.connect(self._editingFinished)
- self._distanceLB.toggled.connect(self._editingFinished)
+ self._sampleDetectorDistanceMetricEntry.editingFinished.connect(
+ self._editingFinished
+ )
+ self._sampleDetectorDistanceLB.toggled.connect(self._editingFinished)
+ self._sourceSampleDistanceMetricEntry.editingFinished.connect(
+ self._editingFinished
+ )
+ self._sourceSampleDistanceLB.toggled.connect(self._editingFinished)
self._fieldOfViewCB.currentIndexChanged.connect(self._editingFinished)
self._fieldOfViewLB.toggled.connect(self._editingFinished)
self._xFlippedCB.toggled.connect(self._editingFinished)
@@ -244,7 +271,8 @@ class NXtomoEditor(qt.QWidget):
"pixel size": self._updatePixelSize,
"frame flips": self._updateFlipped,
"field of view": self._updateFieldOfView,
- "sample-detector distance": self._updateDistance,
+ "sample-detector distance": self._updateSampleDetectorDistance,
+ "source-sample distance": self._updateSourceSampleDistance,
}.items():
try:
fct(scan=scan)
@@ -325,10 +353,16 @@ class NXtomoEditor(qt.QWidget):
if (not self._yFlippedLB.isLocked()) and flip_ud is not None:
self._yFlippedCB.setChecked(flip_ud)
- def _updateDistance(self, scan: NXtomoScan) -> None:
- if not self._distanceLB.isLocked():
+ def _updateSampleDetectorDistance(self, scan: NXtomoScan) -> None:
+ if not self._sampleDetectorDistanceLB.isLocked():
# if in ''auto mode: we want to overwrite the NXtomo existing value by the one of the GUI
- self._distanceMetricEntry.setValue(scan.sample_detector_distance)
+ self._sampleDetectorDistanceMetricEntry.setValue(
+ scan.sample_detector_distance
+ )
+
+ def _updateSourceSampleDistance(self, scan: NXtomoScan) -> None:
+ if not self._sourceSampleDistanceLB.isLocked():
+ self._sourceSampleDistanceMetricEntry.setValue(scan.source_sample_distance)
def _updateEnergy(self, scan: NXtomoScan) -> None:
assert isinstance(scan, NXtomoScan)
@@ -400,8 +434,12 @@ class NXtomoEditor(qt.QWidget):
self._yPixelSizeLB.isLocked(),
),
NXtomoEditorKeys.SAMPLE_DETECTOR_DISTANCE: (
- self._distanceMetricEntry.getValue(),
- self._distanceLB.isLocked(),
+ self._sampleDetectorDistanceMetricEntry.getValue(),
+ self._sampleDetectorDistanceLB.isLocked(),
+ ),
+ NXtomoEditorKeys.SOURCE_SAMPLE_DISTANCE: (
+ self._sourceSampleDistanceMetricEntry.getValue(),
+ self._sourceSampleDistanceLB.isLocked(),
),
NXtomoEditorKeys.FIELD_OF_VIEW: (
self._fieldOfViewCB.currentText(),
@@ -441,9 +479,15 @@ class NXtomoEditor(qt.QWidget):
detector_sample_distance = config.get("instrument.detector.distance", None)
if detector_sample_distance is not None:
detector_sample_distance, distance_locked = detector_sample_distance
- self._distanceMetricEntry.setValue(detector_sample_distance)
+ self._sampleDetectorDistanceMetricEntry.setValue(detector_sample_distance)
self._sampleDetectorDistanceLB.setLock(distance_locked)
+ source_sample_distance = config.get("instrument.source.distance", None)
+ if source_sample_distance is not None:
+ source_sample_distance, distance_locked = source_sample_distance
+ self._sourceSampleDistanceMetricEntry.setValue(source_sample_distance)
+ self._sourceSampleDistanceLB.setLock(distance_locked)
+
field_of_view = config.get("instrument.detector.field_of_view", None)
if field_of_view is not None:
field_of_view, field_of_view_locked = field_of_view
diff --git a/src/tomwer/gui/edit/tests/test_nx_editor.py b/src/tomwer/gui/edit/tests/test_nx_editor.py
index ade4095c4c..71688de70c 100644
--- a/src/tomwer/gui/edit/tests/test_nx_editor.py
+++ b/src/tomwer/gui/edit/tests/test_nx_editor.py
@@ -26,7 +26,8 @@ from tomwer.tests.conftest import qtapp # noqa F401
@pytest.mark.parametrize("x_pixel_size", (None, 0.12))
@pytest.mark.parametrize("y_pixel_size", (None, 0.0065))
@pytest.mark.parametrize("field_of_view", FOV.values())
-@pytest.mark.parametrize("distance", (None, 1.2))
+@pytest.mark.parametrize("sample_detector_distance", (None, 1.2))
+@pytest.mark.parametrize("source_sample_distance", (None, 30.2))
@pytest.mark.parametrize("energy", (None, 23.5))
@pytest.mark.parametrize("x_flipped", (True, False))
@pytest.mark.parametrize("y_flipped", (True, False))
@@ -38,7 +39,8 @@ def test_nx_editor(
x_pixel_size,
y_pixel_size,
field_of_view,
- distance,
+ sample_detector_distance,
+ source_sample_distance,
energy,
x_flipped,
y_flipped,
@@ -50,12 +52,13 @@ def test_nx_editor(
nx_tomo.instrument.detector.x_pixel_size = x_pixel_size
nx_tomo.instrument.detector.y_pixel_size = y_pixel_size
nx_tomo.instrument.detector.field_of_view = field_of_view
- nx_tomo.instrument.detector.distance = distance
+ nx_tomo.instrument.detector.distance = sample_detector_distance
nx_tomo.energy = energy
nx_tomo.sample.x_translation = x_translation
nx_tomo.sample.z_translation = z_translation
nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
nx_tomo.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
+ nx_tomo.instrument.source.distance = source_sample_distance
nx_tomo.sample.rotation_angle = numpy.linspace(0, 20, num=12)
nx_tomo.instrument.detector.transformations.add_transformation(
@@ -89,8 +92,14 @@ def test_nx_editor(
assert check_metric(y_pixel_size, widget._yPixelSizeMetricEntry.getValue())
assert widget._yPixelSizeMetricEntry._qcbUnit.currentText() == "m"
- assert check_metric(distance, widget._distanceMetricEntry.getValue())
- assert widget._distanceMetricEntry._qcbUnit.currentText() == "m"
+ assert check_metric(
+ sample_detector_distance, widget._sampleDetectorDistanceMetricEntry.getValue()
+ )
+ assert widget._sampleDetectorDistanceMetricEntry._qcbUnit.currentText() == "m"
+ assert check_metric(
+ source_sample_distance, widget._sourceSampleDistanceMetricEntry.getValue()
+ )
+ assert widget._sourceSampleDistanceMetricEntry._qcbUnit.currentText() == "m"
assert field_of_view == widget._fieldOfViewCB.currentText()
assert x_flipped == widget._xFlippedCB.isChecked()
@@ -120,7 +129,8 @@ def test_nx_editor(
widget._energyEntry.setText("23.789")
widget._xPixelSizeMetricEntry.setUnit("nm")
widget._yPixelSizeMetricEntry.setValue(2.1e-7)
- widget._distanceMetricEntry.setValue("unknown")
+ widget._sampleDetectorDistanceMetricEntry.setValue("unknown")
+ widget._sourceSampleDistanceMetricEntry.setValue("unknown")
widget._fieldOfViewCB.setCurrentText(FOV.HALF.value)
widget._xFlippedCB.setChecked(not x_flipped)
widget._xTranslationQLE.setValue(1.8)
@@ -204,6 +214,7 @@ def test_nx_editor_lock(
nx_tomo_1.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
nx_tomo_1.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
nx_tomo_1.sample.rotation_angle = numpy.linspace(0, 20, num=12)
+ nx_tomo_1.instrument.source.distance = 1.1
file_path = os.path.join(tmp_path, "nxtomo.nx")
entry = "entry0000"
@@ -229,6 +240,7 @@ def test_nx_editor_lock(
nx_tomo_2.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
nx_tomo_2.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
nx_tomo_2.sample.rotation_angle = numpy.linspace(0, 20, num=12)
+ nx_tomo_2.instrument.source.distance = 6.02
file_path = os.path.join(tmp_path, "nxtomo.nx")
entry = "entry0001"
@@ -251,7 +263,8 @@ def test_nx_editor_lock(
assert widget._energyEntry.getValue() == 5.9
assert widget._xPixelSizeMetricEntry.getValue() == 0.023
assert widget._yPixelSizeMetricEntry.getValue() == 0.025
- assert widget._distanceMetricEntry.getValue() == 2.4
+ assert widget._sampleDetectorDistanceMetricEntry.getValue() == 2.4
+ assert widget._sourceSampleDistanceMetricEntry.getValue() == 1.1
assert widget._fieldOfViewCB.currentText() == "Full"
assert not widget._xFlippedCB.isChecked()
assert widget._yFlippedCB.isChecked()
@@ -286,6 +299,10 @@ def test_nx_editor_lock(
overwrite_nx_tomo.instrument.detector.distance.value
== nx_tomo_1.instrument.detector.distance.value
)
+ assert (
+ overwrite_nx_tomo.instrument.source.distance.value
+ == nx_tomo_1.instrument.source.distance.value
+ )
assert (
overwrite_nx_tomo.instrument.detector.x_flipped
== nx_tomo_1.instrument.detector.x_flipped
@@ -306,6 +323,7 @@ def test_nx_editor_lock(
"instrument.detector.y_flipped": (True, True),
"sample.x_translation": (None,),
"sample.z_translation": (None,),
+ "instrument.source.distance": (1.1, True),
}
for lockerButton in widget._lockerPBs:
@@ -321,6 +339,7 @@ def test_nx_editor_lock(
"instrument.detector.y_flipped": (True, False),
"sample.x_translation": (None,),
"sample.z_translation": (None,),
+ "instrument.source.distance": (1.1, False),
}
@@ -361,7 +380,7 @@ def test_nxtomo_editor_with_missing_paths(
widget.setScan(scan=scan)
- widget._distanceMetricEntry.setValue(0.05)
+ widget._sampleDetectorDistanceMetricEntry.setValue(0.05)
widget._energyEntry.setValue(50)
widget._xPixelSizeMetricEntry.setValue(0.02)
widget._yPixelSizeMetricEntry.setValue(0.03)
diff --git a/src/tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py b/src/tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py
index c03a4ec35f..998ef0e68d 100644
--- a/src/tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py
+++ b/src/tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py
@@ -54,8 +54,8 @@ def test_nx_editor(
assert check_metric(2.5e-6, widget._yPixelSizeMetricEntry.getValue())
assert widget._yPixelSizeMetricEntry._qcbUnit.currentText() == "m"
- assert check_metric(59, widget._distanceMetricEntry.getValue())
- assert widget._distanceMetricEntry._qcbUnit.currentText() == "m"
+ assert check_metric(59, widget._sampleDetectorDistanceMetricEntry.getValue())
+ assert widget._sampleDetectorDistanceMetricEntry._qcbUnit.currentText() == "m"
assert "Half" == widget._fieldOfViewCB.currentText()
assert widget._xFlippedCB.isChecked()
diff --git a/src/tomwer/tasks/edit/nxtomoeditor.py b/src/tomwer/tasks/edit/nxtomoeditor.py
index bd4c30aaae..b99489fe98 100644
--- a/src/tomwer/tasks/edit/nxtomoeditor.py
+++ b/src/tomwer/tasks/edit/nxtomoeditor.py
@@ -36,6 +36,7 @@ class NXtomoEditorKeys:
X_PIXEL_SIZE = "instrument.detector.x_pixel_size"
Y_PIXEL_SIZE = "instrument.detector.y_pixel_size"
SAMPLE_DETECTOR_DISTANCE = "instrument.detector.distance"
+ SOURCE_SAMPLE_DISTANCE = "instrument.source.distance"
FIELD_OF_VIEW = "instrument.detector.field_of_view"
X_FLIPPED = "instrument.detector.x_flipped"
Y_FLIPPED = "instrument.detector.y_flipped"
@@ -272,6 +273,20 @@ class NXtomoEditorTask(
name="sample detector distance",
n_value=1,
),
+ # source / sample distance
+ NXtomoEditorKeys.SOURCE_SAMPLE_DISTANCE: _EditorFieldInfo(
+ nexus_path="/".join(
+ [
+ nexus_paths.INSTRUMENT_PATH,
+ nexus_paths.nx_instrument_paths.SOURCE,
+ nexus_paths.nx_source_paths.DISTANCE,
+ ]
+ ),
+ expected_type=float,
+ units="m",
+ name="source sample distance",
+ n_value=1,
+ ),
# overwrite FOV
NXtomoEditorKeys.FIELD_OF_VIEW: _EditorFieldInfo(
nexus_path=nexus_paths.FOV_PATH,
diff --git a/src/tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py b/src/tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py
index cb79ae76eb..547083afa5 100644
--- a/src/tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py
+++ b/src/tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py
@@ -29,6 +29,7 @@ def getDefaultConfig() -> dict:
NXtomoEditorKeys.Y_FLIPPED: (False, False),
NXtomoEditorKeys.X_TRANSLATION: (0.0,),
NXtomoEditorKeys.Z_TRANSLATION: (0.0,),
+ NXtomoEditorKeys.SOURCE_SAMPLE_DISTANCE: (1.3, True),
}
@@ -50,10 +51,10 @@ def test_NXtomoEditorOW(
signal_listener = SignalListener()
window.sigScanReady.connect(signal_listener)
# set up the widget to define and lock distance, energy and x pixel size
- distance_widget = window.widget.mainWidget._distanceMetricEntry
+ distance_widget = window.widget.mainWidget._sampleDetectorDistanceMetricEntry
distance_widget.setValue(0.6)
distance_widget.setUnit("mm")
- distance_locker = window.widget.mainWidget._distanceLB
+ distance_locker = window.widget.mainWidget._sampleDetectorDistanceLB
distance_locker.setLock(True)
energy_widget = window.widget.mainWidget._energyEntry
energy_widget.setValue(88.058)
--
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