tomwer 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py

@@ -0,0 +1,72 @@
+import os
+import pytest
+import numpy
+from tomoscan.esrf.scan.hdf5scan import ImageKey
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
+from nxtomomill.nexus.nxtomo import NXtomo
+from tomwer.tests.conftest import qtapp  # noqa F401
+from silx.gui import qt
+
+
+def test_nx_editor(
+    tmp_path,
+    qtapp,  # noqa F811
+):
+    # 1.0 create nx tomo with raw data
+    nx_tomo = NXtomo()
+    nx_tomo.instrument.detector.x_pixel_size = 2.6e-6
+    nx_tomo.instrument.detector.y_pixel_size = 2.5e-6
+    nx_tomo.instrument.detector.field_of_view = "Half"
+    nx_tomo.instrument.detector.distance = 59.0
+    nx_tomo.instrument.detector.x_flipped = True
+    nx_tomo.instrument.detector.y_flipped = False
+    nx_tomo.energy = 12.8
+    nx_tomo.sample.x_translation = numpy.arange(12)
+    nx_tomo.sample.z_translation = numpy.arange(2, 14)
+    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, 180, num=12)
+
+    file_path = os.path.join(tmp_path, "nxtomo.nx")
+    entry = "entry0000"
+    nx_tomo.save(
+        file_path=file_path,
+        data_path=entry,
+    )
+
+    scan = HDF5TomoScan(file_path, entry)
+
+    # 2.0 create the widget and do the edition
+    widget = NXtomoMetadataViewer()
+    widget.setScan(scan=scan)
+    widget.show()
+
+    # 3.0 check data have been corrcetly loaded
+    def check_metric(expected_value, current_value):
+        if expected_value is None:
+            return current_value is None
+        return expected_value == current_value
+
+    assert check_metric(2.6e-6, widget._xPixelSizeMetricEntry.getValue())
+    assert widget._xPixelSizeMetricEntry._qcbUnit.currentText() == "m"
+    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 "Half" == widget._fieldOfViewCB.currentText()
+    assert widget._xFlippedCB.isChecked()
+    assert not widget._yFlippedCB.isChecked()
+
+    assert "12.8" == widget._energyQLE.text()
+
+    # make sure saving raises an error (viewer inherit from the editor)
+    with pytest.raises(NotImplementedError):
+        widget.overwriteNXtomo()
+
+    # end
+    widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+    widget.close()
+    widget = None

tomwer/gui/visualization/test/test_stacks.py

@@ -38,7 +38,7 @@ import logging
 import time
 import pytest
 from tomoscan.esrf.volume.edfvolume import EDFVolume
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 import weakref
 
 logging.disable(logging.INFO)

tomwer/gui/visualization/tomoobjoverview.py

@@ -0,0 +1,49 @@
+from .volumeoverview import VolumeOverviewWidget
+from .scanoverview import ScanOverviewWidget
+from silx.gui import qt
+from tomwer.core.tomwer_object import TomwerObject
+from tomwer.core.volume.volumebase import TomwerVolumeBase
+from tomwer.core.scan.scanbase import TomwerScanBase
+from typing import Optional
+
+
+class TomoObjOverview(qt.QWidget):
+    """
+    Dummy widget to show ScanOverviewWidget if the object is a scan or VolumeOverviewWidget if the object is a Volume
+    """
+
+    def __init__(self, parent=None) -> None:
+        super().__init__(parent)
+        self.setLayout(qt.QVBoxLayout())
+        self._scanOverview = ScanOverviewWidget(self)
+        self.layout().addWidget(self._scanOverview)
+
+        self._volumeOverview = VolumeOverviewWidget(self)
+        self.layout().addWidget(self._volumeOverview)
+
+        self._scanOverview.setVisible(False)
+        self._volumeOverview.setVisible(False)
+
+    def setTomoObj(self, tomo_obj: Optional[TomwerObject]):
+        """
+        update sub widgets according to the type of tomo_obj
+        """
+        if tomo_obj is not None and not isinstance(tomo_obj, TomwerObject):
+            raise TypeError(
+                f"tomo_obj is expected to be an instance of {TomwerObject} and not {type(tomo_obj)}"
+            )
+        # handle visibility
+        self._volumeOverview.setVisible(isinstance(tomo_obj, TomwerVolumeBase))
+        self._scanOverview.setVisible(isinstance(tomo_obj, TomwerScanBase))
+
+        if isinstance(tomo_obj, TomwerVolumeBase):
+            self._scanOverview.setScan(None)
+            self._volumeOverview.setVolume(tomo_obj)
+        elif isinstance(tomo_obj, TomwerScanBase):
+            self._scanOverview.setScan(tomo_obj)
+            self._volumeOverview.setVolume(None)
+        elif tomo_obj is None:
+            self._volumeOverview.setVolume(None)
+            self._scanOverview.setScan(None)
+        else:
+            raise RuntimeError(f"TomwerObject of type {type(tomo_obj)} is not handled")

tomwer/gui/visualization/volumeoverview.py

@@ -0,0 +1,64 @@
+from silx.gui import qt
+from tomwer.core.volume.volumebase import TomwerVolumeBase
+from tomoscan.identifier import VolumeIdentifier
+from typing import Optional
+import logging
+
+_logger = logging.getLogger(__name__)
+
+
+class VolumeOverviewWidget(qt.QWidget):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self._volumeIdentifier = None
+        self.setLayout(qt.QVBoxLayout())
+        self._tree = qt.QTreeWidget(self)
+        self._tree.setColumnCount(2)
+        self._tree.setHeaderLabels(("metadata", "value"))
+        self.layout().addWidget(self._tree)
+
+        # 1: define translations
+        self._x_position = qt.QTreeWidgetItem(self._tree)
+        self._x_position.setText(0, "x position")
+        self._y_position = qt.QTreeWidgetItem(self._tree)
+        self._y_position.setText(0, "y position")
+        self._z_position = qt.QTreeWidgetItem(self._tree)
+        self._z_position.setText(0, "z position")
+
+        # 2. define pixel size
+        self._x_pixel_size = qt.QTreeWidgetItem(self._tree)
+        self._x_pixel_size.setText(0, "x pixel size")
+        self._y_pixel_size = qt.QTreeWidgetItem(self._tree)
+        self._y_pixel_size.setText(0, "y pixel size")
+
+    def setVolume(self, volume: Optional[TomwerVolumeBase]):
+        if volume is None:
+            self._x_position.setText(1, "")
+            self._y_position.setText(1, "")
+            self._z_position.setText(1, "")
+            self._x_pixel_size.setText(1, "")
+            self._y_pixel_size.setText(1, "")
+        elif not isinstance(volume, TomwerVolumeBase):
+            raise TypeError(
+                f"volume is expected to be a {TomwerVolumeBase} or a {VolumeIdentifier}. Not ({type(volume)}) "
+            )
+        else:
+            try:
+                x_pos, y_pos, z_pos = volume.position()
+            except Exception:
+                self._x_position.setText(1, "?")
+                self._y_position.setText(1, "?")
+                self._z_position.setText(1, "?")
+            else:
+                self._x_position.setText(1, x_pos)
+                self._y_position.setText(1, y_pos)
+                self._z_position.setText(1, z_pos)
+
+            try:
+                x_size, y_size = volume.pixel_size
+            except Exception:
+                self._x_pixel_size.setText(1, "?")
+                self._y_pixel_size.setText(1, "?")
+            else:
+                self._x_pixel_size.setText(1, x_size)
+                self._y_pixel_size.setText(1, y_size)

tomwer/gui/visualization/volumeviewer.py

@@ -336,7 +336,7 @@ class VolumeViewer(qt.QMainWindow):
                 pass
             else:
                 raise TypeError(
-                    "Volume should be an instance of a Volume, a VolumeIdentifier or a string refering to a VolumeIdentifier"
+                    f"Volume should be an instance of a Volume, a VolumeIdentifier or a string refering to a VolumeIdentifier. {type(volume)} provided"
                 )
 
             data = self._get_data_volume(volume)

tomwer/io/utils/utils.py

@@ -199,7 +199,7 @@ def get_linked_files_with_entry(hdf5_file: str, entry: str) -> set:
     while len(items_to_treat) > 0:
         to_treat = list(items_to_treat)
         items_to_treat.clear()
-        for (abs_file_path, file_path, data_path) in to_treat:
+        for abs_file_path, file_path, data_path in to_treat:
             item = abs_file_path, data_path
             if item in treated_items:
                 continue
@@ -250,7 +250,7 @@ def get_linked_files_with_vds(hdf5_file: str, dataset_path: str) -> set:
     while len(items_to_treat) > 0:
         to_treat = list(items_to_treat)
         items_to_treat.clear()
-        for (abs_file_path, file_path, dataset_path) in to_treat:
+        for abs_file_path, file_path, dataset_path in to_treat:
             item = abs_file_path, dataset_path
             if item in treated_items:
                 continue

tomwer/resources/gui/icons/multi-document-save.svg

@@ -0,0 +1,101 @@
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