tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/gui/edit/{test → tests}/test_nx_editor.py

@@ -12,11 +12,12 @@ from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.nxdetector import ImageKey, FOV
 from nxtomo.utils.transformation import (
     build_matrix,
-    UDDetTransformation,
-    LRDetTransformation,
+    DetYFlipTransformation,
+    DetZFlipTransformation,
 )
 from nxtomo.nxobject.nxtransformations import NXtransformations
 
+from tomwer.core.process.edit.nxtomoeditor import NXtomoEditorTask
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.gui.edit.nxtomoeditor import NXtomoEditor, _TranslationMetricEntry
 from tomwer.tests.conftest import qtapp  # noqa F401
@@ -56,14 +57,13 @@ def test_nx_editor(
     nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
     nx_tomo.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
     nx_tomo.sample.rotation_angle = numpy.linspace(0, 20, num=12)
-    if x_flipped:
-        nx_tomo.instrument.detector.transformations.add_transformation(
-            LRDetTransformation()
-        )
-    if y_flipped:
-        nx_tomo.instrument.detector.transformations.add_transformation(
-            UDDetTransformation()
-        )
+
+    nx_tomo.instrument.detector.transformations.add_transformation(
+        DetZFlipTransformation(flip=x_flipped)
+    )
+    nx_tomo.instrument.detector.transformations.add_transformation(
+        DetYFlipTransformation(flip=y_flipped)
+    )
 
     file_path = os.path.join(tmp_path, "nxtomo.nx")
     entry = "entry0000"
@@ -78,7 +78,7 @@ def test_nx_editor(
     widget = NXtomoEditor()
     widget.setScan(scan=scan)
 
-    # 3.0 check data have been corrcetly loaded
+    # 3.0 check data have been correctly loaded
     def check_metric(expected_value, current_value):
         if expected_value is None:
             return current_value is None
@@ -128,8 +128,14 @@ def test_nx_editor(
     widget._zTranslationQLE.setValue(2.8)
     widget._zTranslationQLE.setUnit("m")
 
-    # 5.0 save
-    widget.overwriteNXtomo()
+    # 5.0
+    task = NXtomoEditorTask(
+        inputs={
+            "data": scan,
+            "configuration": widget.getConfigurationForTask(),
+        }
+    )
+    task.run()
 
     # 6.0 make sure data have been overwrite
     overwrite_nx_tomo = NXtomo().load(
@@ -139,24 +145,24 @@ def test_nx_editor(
 
     assert overwrite_nx_tomo.energy.value == 23.789
     assert overwrite_nx_tomo.energy.unit == EnergySI.KILOELECTRONVOLT
+
     if x_pixel_size is None:
         assert overwrite_nx_tomo.instrument.detector.x_pixel_size.value is None
     else:
         assert numpy.isclose(
-            overwrite_nx_tomo.instrument.detector.x_pixel_size.value,
+            overwrite_nx_tomo.instrument.detector.x_pixel_size.si_value,
             x_pixel_size * MetricSystem.NANOMETER.value,
         )
-    assert overwrite_nx_tomo.instrument.detector.y_pixel_size.value == 2.1e-7
+    assert overwrite_nx_tomo.instrument.detector.y_pixel_size.si_value == 2.1e-7
 
     assert overwrite_nx_tomo.instrument.detector.distance.value is None
     assert overwrite_nx_tomo.instrument.detector.field_of_view is FOV.HALF
 
     final_transformation = NXtransformations()
 
-    if y_flipped:
-        final_transformation.add_transformation(UDDetTransformation())
-    if not x_flipped:  # as we invert _xFlippedCB combobox
-        final_transformation.add_transformation(LRDetTransformation())
+    final_transformation.add_transformation(DetYFlipTransformation(flip=y_flipped))
+    final_transformation.add_transformation(DetZFlipTransformation(flip=not x_flipped))
+    # note: the 'not' comes from inversion done with the _xFlippedCB combobox
 
     numpy.testing.assert_allclose(
         build_matrix(
@@ -166,12 +172,12 @@ def test_nx_editor(
     )
 
     numpy.testing.assert_array_almost_equal(
-        overwrite_nx_tomo.sample.x_translation.value,
+        overwrite_nx_tomo.sample.x_translation.si_value,
         numpy.array([1.8 * MetricSystem.MILLIMETER.value] * 12),
     )
     assert overwrite_nx_tomo.sample.x_translation.unit is MetricSystem.METER
     numpy.testing.assert_array_almost_equal(
-        overwrite_nx_tomo.sample.z_translation.value,
+        overwrite_nx_tomo.sample.z_translation.si_value,
         numpy.array([2.8 * MetricSystem.METER.value] * 12),
     )
     assert overwrite_nx_tomo.sample.z_translation.unit is MetricSystem.METER
@@ -251,7 +257,13 @@ def test_nx_editor_lock(
     assert widget._yFlippedCB.isChecked()
 
     # 3.0 save the nxtomo
-    widget.overwriteNXtomo()
+    task = NXtomoEditorTask(
+        inputs={
+            "data": scan_2,
+            "configuration": widget.getConfigurationForTask(),
+        }
+    )
+    task.run()
 
     # 4.0 check save went well
     overwrite_nx_tomo = NXtomo().load(
@@ -292,6 +304,8 @@ def test_nx_editor_lock(
         "instrument.detector.y_pixel_size": (0.025, True),
         "instrument.detector.x_flipped": (False, True),
         "instrument.detector.y_flipped": (True, True),
+        "sample.x_translation": (None,),
+        "sample.z_translation": (None,),
     }
 
     for lockerButton in widget._lockerPBs:
@@ -305,6 +319,8 @@ def test_nx_editor_lock(
         "instrument.detector.y_pixel_size": (0.025, False),
         "instrument.detector.x_flipped": (False, False),
         "instrument.detector.y_flipped": (True, False),
+        "sample.x_translation": (None,),
+        "sample.z_translation": (None,),
     }
 
 
@@ -351,7 +367,13 @@ def test_nxtomo_editor_with_missing_paths(
     widget._yPixelSizeMetricEntry.setValue(0.03)
 
     # overwrite the NXtomo
-    widget.overwriteNXtomo()
+    task = NXtomoEditorTask(
+        inputs={
+            "data": scan,
+            "configuration": widget.getConfigurationForTask(),
+        }
+    )
+    task.run()
 
     # check save went well
     overwrite_nx_tomo = NXtomo().load(

tomwer/gui/fonts.py

@@ -0,0 +1,5 @@
+from silx.gui import qt
+
+FONT_IMPORTANT = qt.QFont("Arial", 12)
+FONT_MEDIUM = qt.QFont("Arial", 10)
+FONT_SMALL = qt.QFont("Arial", 8)

tomwer/gui/icons.py

@@ -1,36 +1,9 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
 """Set of icons for buttons.
 
 Use :func:`getQIcon` to create Qt QIcon from the name identifying an icon.
 """
 
-__authors__ = ["T. Vincent"]
-__license__ = "MIT"
-__date__ = "06/09/2017"
-
 
 import logging
 import os
@@ -62,7 +35,7 @@ class AbstractAnimatedIcon(qt.QObject):
     def __init__(self, parent=None):
         """Constructor
 
-        :param qt.QObject parent: Parent of the QObject
+        :param parent: Parent of the QObject
         :raises: ValueError when name is not known
         """
         qt.QObject.__init__(self, parent)
@@ -71,14 +44,14 @@ class AbstractAnimatedIcon(qt.QObject):
         self.__currentIcon = None
 
     iconChanged = qt.Signal(qt.QIcon)
-    """Signal sent with a QIcon everytime the animation changed."""
+    """Signal sent with a QIcon every time the animation changed."""
 
     def register(self, obj):
         """Register an object to the AnimatedIcon.
-        If no object are registred, the animation is paused.
+        If no object are registered, the animation is paused.
         Object are stored in a weaked list.
 
-        :param object obj: An object
+        :param obj: An object
         """
         if obj not in self.__targets:
             self.__targets.append(obj)
@@ -86,7 +59,7 @@ class AbstractAnimatedIcon(qt.QObject):
 
     def unregister(self, obj):
         """Remove the object from the registration.
-        If no object are registred the animation is paused.
+        If no object are registered the animation is paused.
 
         :param object obj: A registered object
         """
@@ -94,26 +67,19 @@ class AbstractAnimatedIcon(qt.QObject):
             self.__targets.remove(obj)
         self._updateState()
 
-    def hasRegistredObjects(self):
-        """Returns true if any object is registred.
-
-        :rtype: bool
-        """
+    def hasRegistredObjects(self) -> bool:
+        """Returns true if any object is registered."""
         return len(self.__targets)
 
-    def isRegistered(self, obj):
-        """Returns true if the object is registred in the AnimatedIcon.
+    def isRegistered(self, obj) -> bool:
+        """Returns true if the object is registered in the AnimatedIcon.
 
         :param object obj: An object
-        :rtype: bool
         """
         return obj in self.__targets
 
-    def currentIcon(self):
-        """Returns the icon of the current frame.
-
-        :rtype: qt.QIcon
-        """
+    def currentIcon(self) -> qt.QIcon:
+        """Returns the icon of the current frame."""
         return self.__currentIcon
 
     def _updateState(self):
@@ -131,14 +97,14 @@ class AbstractAnimatedIcon(qt.QObject):
 
 class MovieAnimatedIcon(AbstractAnimatedIcon):
     """Store a looping QMovie to provide icons for each frames.
-    Provides an event with the new icon everytime the movie frame
+    Provides an event with the new icon every time the movie frame
     is updated."""
 
     def __init__(self, filename, parent=None):
         """Constructor
 
-        :param str filename: An icon name to an animated format
-        :param qt.QObject parent: Parent of the QObject
+        :param filename: An icon name to an animated format
+        :param parent: Parent of the QObject
         :raises: ValueError when name is not known
         """
         AbstractAnimatedIcon.__init__(self, parent)
@@ -153,8 +119,8 @@ class MovieAnimatedIcon(AbstractAnimatedIcon):
         self.__updateIconAtFrame(0)
 
     def __frameChanged(self, frameId):
-        """Callback everytime the QMovie frame change
-        :param int frameId: Current frame id
+        """Callback every time the QMovie frame change
+        :param frameId: Current frame id
         """
         self.__updateIconAtFrame(frameId)
 
@@ -162,7 +128,7 @@ class MovieAnimatedIcon(AbstractAnimatedIcon):
         """
         Update the current stored QIcon
 
-        :param int frameId: Current frame id
+        :param frameId: Current frame id
         """
         if frameId in self.__cacheIcons:
             icon = self.__cacheIcons[frameId]
@@ -179,14 +145,14 @@ class MovieAnimatedIcon(AbstractAnimatedIcon):
 
 class MultiImageAnimatedIcon(AbstractAnimatedIcon):
     """Store a looping QMovie to provide icons for each frames.
-    Provides an event with the new icon everytime the movie frame
+    Provides an event with the new icon every time the movie frame
     is updated."""
 
     def __init__(self, filename, parent=None):
         """Constructor
 
-        :param str filename: An icon name to an animated format
-        :param qt.QObject parent: Parent of the QObject
+        :param filename: An icon name to an animated format
+        :param parent: Parent of the QObject
         :raises: ValueError when name is not known
         """
         AbstractAnimatedIcon.__init__(self, parent)
@@ -219,7 +185,7 @@ class MultiImageAnimatedIcon(AbstractAnimatedIcon):
         """
         Update the current stored QIcon
 
-        :param int frameId: Current frame id
+        :param frameId: Current frame id
         """
         self.__frameId = frameId
         icon = self.__frames[frameId]
@@ -237,7 +203,7 @@ class MultiImageAnimatedIcon(AbstractAnimatedIcon):
 
 class AnimatedIcon(MovieAnimatedIcon):
     """Store a looping QMovie to provide icons for each frames.
-    Provides an event with the new icon everytime the movie frame
+    Provides an event with the new icon every time the movie frame
     is updated.
 
     It may not be available anymore for the silx release 0.6.
@@ -252,10 +218,7 @@ class AnimatedIcon(MovieAnimatedIcon):
 
 
 def getWaitIcon():
-    """Returns a cached version of the waiting AbstractAnimatedIcon.
-
-    :rtype: AbstractAnimatedIcon
-    """
+    """Returns a cached version of the waiting AbstractAnimatedIcon."""
     return getAnimatedIcon("process-working")
 
 
@@ -277,7 +240,7 @@ def getAnimatedIcon(name):
     In Qt5 mng or gif are not used, because the transparency is not very well
     managed.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding AbstractAnimatedIcon
     :raises: ValueError when name is not known
@@ -321,7 +284,7 @@ def getQIcon(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QIcon
     :raises: ValueError when name is not known
@@ -348,7 +311,7 @@ def getQPixmap(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QPixmap
     :raises: ValueError when name is not known
@@ -357,7 +320,7 @@ def getQPixmap(name):
     return qt.QPixmap(qfile.fileName())
 
 
-def getQFile(name):
+def getQFile(name) -> qt.QFile:
     """Create a QFile from an icon name. Filename is found
     according to supported Qt formats.
 
@@ -370,10 +333,9 @@ def getQFile(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QFile
-    :rtype: qt.QFile
     :raises: ValueError when name is not known
     """
     global _supported_formats

tomwer/gui/illustrations.py

@@ -1,37 +1,8 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
 """Set of icons for buttons.
 
 Use :func:`getQIcon` to create Qt QIcon from the name identifying an icon.
 """
 
-__authors__ = ["T. Vincent"]
-__license__ = "MIT"
-__date__ = "06/09/2017"
-
-
 import logging
 import os
 import weakref
@@ -64,7 +35,7 @@ def getQIcon(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QIcon
     :raises: ValueError when name is not known
@@ -87,7 +58,7 @@ def getQPixmap(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QPixmap
     :raises: ValueError when name is not known
@@ -98,7 +69,7 @@ def getQPixmap(name):
     return qt.QPixmap(qfile.fileName())
 
 
-def getQFile(name):
+def getQFile(name) -> qt.QFile:
     """Create a QFile from an icon name. Filename is found
     according to supported Qt formats.
 
@@ -111,10 +82,9 @@ def getQFile(name):
 
     See also :func:`silx.resources.register_resource_directory`.
 
-    :param str name: Name of the icon, in one of the defined icons
+    :param name: Name of the icon, in one of the defined icons
                      in this module.
     :return: Corresponding QFile
-    :rtype: qt.QFile
     :raises: ValueError when name is not known
     """
     # if the extension is given in the name, skip the supported_formats

tomwer/gui/imagefromfile.py

@@ -1,32 +1,7 @@
-# /*##########################################################################
-# Copyright (C) 2016-2017 European Synchrotron Radiation Facility
-#
-# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
-# the ESRF by the Software group.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#############################################################################*/
-
-__author__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "06/08/2018"
+"""Utils to load images from file
+"""
+
+from __future__ import annotations
 
 
 import functools
@@ -147,7 +122,7 @@ class FileWithImage(object):
     def getImages(self, _load):
         """
 
-        :param bool _load: if True then launch the load of the image
+        :param _load: if True then launch the load of the image
         :return: the list of images contained in the given file.
         """
         if self.file.lower().endswith(TomwerScanBase.VALID_RECONS_EXTENSION):

tomwer/gui/metadataloader.py

@@ -0,0 +1,36 @@
+"""Utils to load metadata (from a volume at the moment)
+"""
+
+import logging
+from silx.gui import qt
+from tomwer.core.volume.volumefactory import VolumeFactory
+
+_logger = logging.getLogger(__name__)
+
+__all__ = [
+    "VolumeMetadataLoader",
+]
+
+
+class VolumeMetadataLoader(qt.QThread):
+    """Thread to load metadata from a given volume"""
+
+    def __init__(self, parent, tomo_obj_identifier: str):
+        super().__init__(parent=parent)
+        self.volume = VolumeFactory.create_tomo_object_from_identifier(
+            tomo_obj_identifier
+        )
+        self.metadata = None
+
+    def run(self):
+        try:
+            self.metadata = self.volume.load_metadata()
+        except IOError:
+            self.metadata = None
+        except Exception as e:
+            _logger.error(
+                "Fail to load metadata from %s. Error is %s",
+                self.volume.get_identifier(),
+                e,
+            )
+            self.metadata = None

tomwer/gui/qconfigfile.py

@@ -1,3 +1,6 @@
+"""contains 'QConfigFileDialog': dialog to get / set a .cfg file
+"""
+
 import os
 from silx.gui import qt
 

tomwer/gui/qlefilesystem.py

@@ -1,3 +1,6 @@
+"""contains QLFileSystem class. Specific implementation of the QLineEdit to select a file path.
+"""
+
 from silx.gui import qt
 
 

tomwer/gui/reconstruction/__init__.py

@@ -0,0 +1,2 @@
+"""Widgets related to tomography reconstruction (cor search, nabu volume reconstruction...)
+"""