tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/gui/visualization/diffviewer/diffviewer.py

@@ -42,7 +42,7 @@ from silx.gui import qt
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.image import shift_img
@@ -158,7 +158,7 @@ class _FrameSelector(qt.QWidget):
             if self._scan.flats is not None:
                 urls = self._scan.flats.values()
         elif type_selected == self.FrameType.PROJ:
-            if isinstance(self._scan, HDF5TomoScan):
+            if isinstance(self._scan, NXtomoScan):
                 angles_and_urls = self._scan.get_proj_angle_url(with_alignment=False)
                 for angle, url in angles_and_urls.items():
                     urls.append(url)
@@ -267,10 +267,10 @@ class _FramesSelector(qt.QWidget):
         self._rightSelector.layout().setContentsMargins(0, 0, 0, 0)
 
         # signal / slot connection
-        self._leftSelector.sigCorrectionChanged.connect(self._leftFrameUpdReq)
-        self._rightSelector.sigCorrectionChanged.connect(self._rightFrameUpdReq)
-        self._leftSelector.sigSelectedUrlChanged.connect(self._leftFrameUpdReq)
-        self._rightSelector.sigSelectedUrlChanged.connect(self._rightFrameUpdReq)
+        self._leftSelector.sigCorrectionChanged.connect(self.sigLeftFrameUpdateReq)
+        self._rightSelector.sigCorrectionChanged.connect(self.sigRightFrameUpdateReq)
+        self._leftSelector.sigSelectedUrlChanged.connect(self.sigLeftFrameUpdateReq)
+        self._rightSelector.sigSelectedUrlChanged.connect(self.sigRightFrameUpdateReq)
         self._leftScanCB.sigScanChanged.connect(self._leftScanChanged)
         self._rightScanCB.sigScanChanged.connect(self._rightScanChanged)
         self._leftScanCB.sigRequestScanAdd.connect(self._addScanFrmDialogLeft)
@@ -314,12 +314,6 @@ class _FramesSelector(qt.QWidget):
     def getRightUrl(self):
         return self._rightSelector.getCurrentUrl()
 
-    def _rightFrameUpdReq(self):
-        self.sigRightFrameUpdateReq.emit()
-
-    def _leftFrameUpdReq(self):
-        self.sigLeftFrameUpdateReq.emit()
-
     def _addScanFrmDialogLeft(self):
         self._addScanFrmDialog(link_to="left")
 
@@ -542,7 +536,7 @@ class _ScanComboBox(qt.QWidget):
 
         # connect signal / slot
         self._scansCB.currentIndexChanged.connect(self._scanChanged)
-        self._addButton.pressed.connect(self._addScanCallback)
+        self._addButton.released.connect(self.sigRequestScanAdd)
 
     def clear(self):
         self._scans = set()
@@ -574,6 +568,3 @@ class _ScanComboBox(qt.QWidget):
             return None
         else:
             return scan
-
-    def _addScanCallback(self):
-        self.sigRequestScanAdd.emit()

tomwer/gui/visualization/diffviewer/shiftwidget.py

@@ -91,8 +91,8 @@ class TwoFramesShiftTab(qt.QTabWidget, _FrameShiftsBase):
         self._absoluteShiftWidget = Absolute2FramesShift(self)
         self.addTab(self._absoluteShiftWidget, self.ShiftMode.ABSOLUTE.value)
         # connect signal / slot
-        self._absoluteShiftWidget.sigShiftsChanged.connect(self._propagateSignal)
-        self._relativeShiftWidget.sigShiftsChanged.connect(self._propagateSignal)
+        self._absoluteShiftWidget.sigShiftsChanged.connect(self.sigShiftsChanged)
+        self._relativeShiftWidget.sigShiftsChanged.connect(self.sigShiftsChanged)
         # set up
         self.setCurrentWidget(self._relativeShiftWidget)
         self._relativeShiftWidget.setFocus(qt.Qt.OtherFocusReason)
@@ -102,9 +102,6 @@ class TwoFramesShiftTab(qt.QTabWidget, _FrameShiftsBase):
     def getRelativeShiftWidget(self):
         return self._relativeShiftWidget
 
-    def _propagateSignal(self, shift_infos: tuple):
-        self.sigShiftsChanged.emit(shift_infos)
-
     def getShiftMode(self):
         if self.currentWidget() is self._relativeShiftWidget:
             return self.ShiftMode.RELATIVE

tomwer/gui/visualization/scanoverview.py

@@ -32,7 +32,7 @@ import logging
 import weakref
 
 from silx.gui import qt
-from tomoscan.scanbase import FOV
+from nxtomo.nxobject.nxdetector import FOV
 
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase

tomwer/gui/visualization/sinogramviewer.py

@@ -35,14 +35,8 @@ import logging
 import weakref
 
 from silx.gui import qt
-
-try:
-    from silx.gui.plot.ImageStack import (  # noqa F401
-        PlotWithWaitingLabel as _PlotWithWaitingLabel,
-    )
-except ImportError:
-    from silx.gui.plot.ImageStack import _PlotWithWaitingLabel  # noqa F401
-
+from silx.gui.plot import Plot2D
+from silx.gui.widgets.WaitingOverlay import WaitingOverlay
 from tomwer.gui.settings import Y_AXIS_DOWNWARD
 
 _logger = logging.getLogger(__name__)
@@ -72,13 +66,16 @@ class SinogramViewer(qt.QMainWindow):
         # used to memorize sinogram properties when load it.
         # Contains (str(scan), line, oversampling)
 
-        self._plot = _PlotWithWaitingLabel(parent=self)
-        self._plot.getPlotWidget().setYAxisInverted(Y_AXIS_DOWNWARD)
-        plot = self._plot.getPlotWidget()
-        plot.getDefaultColormap().setVRange(None, None)
-        plot.setAxesDisplayed(False)
-        plot.setKeepDataAspectRatio(True)
-        self._plot.setWaiting(False)
+        self._plot = Plot2D(parent=self)
+        self._plotWaiter = WaitingOverlay(self._plot)
+        self._plotWaiter.hide()
+        self._plotWaiter.setIconSize(qt.QSize(30, 30))
+
+        self._plot.getMaskAction().setVisible(False)
+        self._plot.setYAxisInverted(Y_AXIS_DOWNWARD)
+        self._plot.getDefaultColormap().setVRange(None, None)
+        self._plot.setAxesDisplayed(False)
+        self._plot.setKeepDataAspectRatio(True)
         self._dockOpt = qt.QDockWidget(self)
         self._options = SinogramOpts(parent=self, orientation=opts_orientation)
         self._dockOpt.setWidget(self._options)
@@ -95,7 +92,7 @@ class SinogramViewer(qt.QMainWindow):
         self._loadingThread.finished.connect(self._sinogram_loaded)
 
         # expose API
-        self.getActiveImage = plot.getActiveImage
+        self.getActiveImage = self._plot.getActiveImage
 
         # set up
         if scan is not None:
@@ -131,18 +128,12 @@ class SinogramViewer(qt.QMainWindow):
         self._options.setSubsampling(value)
 
     def _updatePlot(self, sinogram):
-        self._plot.getPlotWidget().addImage(data=sinogram)
-        self._plot.getPlotWidget().replot()
-
-    def _editionLocked(self, locked):
-        self.sigAxisEditionLocked.emit(locked)
-
-    def _applyRequested(self):
-        self.sigApply.emit()
+        self._plot.addImage(data=sinogram)
+        self._plot.replot()
 
     def _sinogram_loaded(self):
         """callback when the sinogram is loaded"""
-        self._plot.setWaiting(False)
+        self._plotWaiter.hide()
         if self._scan is None or self._scan() is None:
             return
         assert self._sinoInfoCache is not None
@@ -167,7 +158,7 @@ class SinogramViewer(qt.QMainWindow):
             )
             return
         # update scan
-        self._plot.setWaiting(True)
+        self._plotWaiter.show()
         self.sigSinoLoadStarted.emit()
         self._sinoInfoCache = (
             str(self._scan()),
@@ -182,18 +173,14 @@ class SinogramViewer(qt.QMainWindow):
         self._loadingThread.start()
 
     def clear(self):
-        self._plot.getPlotWidget().clear()
+        self._plot.clear()
 
     def close(self):
-        self._stopAnimationThread()
+        self._plotWaiter.hide()
         self._plot.close()
         self._plot = None
         super().close()
 
-    def _stopAnimationThread(self):
-        if self._plot is not None:
-            self._plot.stopUpdateThread()
-
 
 class _LoadSinoThread(qt.QThread):
     def init(self, data, line, subsampling):
@@ -272,15 +259,12 @@ class SinogramOpts(qt.QDialog):
 
         # connect signal / slot
         self._buttons.button(qt.QDialogButtonBox.Apply).clicked.connect(
-            self._updateSinogram
+            self.sigUpdateRequested
         )
 
     def setLineSelectionVisible(self, visible):
         self._lineSelWidget.setVisible(visible)
 
-    def _updateSinogram(self):
-        self.sigUpdateRequested.emit()
-
     def setScan(self, scan):
         old = self.blockSignals(True)
         # update line max and value

tomwer/gui/visualization/test/test_diffviewer.py

@@ -37,7 +37,7 @@ import unittest
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
 
-from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.core.utils.scanutils import MockNXtomo
 from tomwer.gui.visualization.diffviewer import DiffFrameViewer
 
 logging.disable(logging.INFO)
@@ -52,14 +52,14 @@ class TestDiffViewer(TestCaseQt):
         self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
 
         self.tmp_dir = tempfile.mkdtemp()
-        self.scan1 = MockHDF5(
+        self.scan1 = MockNXtomo(
             scan_path=os.path.join(self.tmp_dir, "myscan"),
             n_proj=20,
             n_ini_proj=20,
             dim=10,
         ).scan
 
-        self.scan2 = MockHDF5(
+        self.scan2 = MockNXtomo(
             scan_path=os.path.join(self.tmp_dir, "myscan"),
             n_proj=20,
             n_ini_proj=20,

tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py

@@ -2,11 +2,11 @@ import os
 
 import numpy
 import pytest
-from nxtomomill.nexus.nxtomo import NXtomo
+from nxtomo.application.nxtomo import NXtomo
 from silx.gui import qt
-from tomoscan.esrf.scan.hdf5scan import ImageKey
+from nxtomo.nxobject.nxdetector import ImageKey
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
 from tomwer.tests.conftest import qtapp  # noqa F401
 
@@ -37,7 +37,7 @@ def test_nx_editor(
         data_path=entry,
     )
 
-    scan = HDF5TomoScan(file_path, entry)
+    scan = NXtomoScan(file_path, entry)
 
     # 2.0 create the widget and do the edition
     widget = NXtomoMetadataViewer()

tomwer/gui/visualization/test/test_sinogramviewer.py

@@ -38,7 +38,7 @@ import unittest
 from silx.gui import qt
 from silx.gui.utils.testutils import SignalListener, TestCaseQt
 
-from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.core.utils.scanutils import MockNXtomo
 from tomwer.gui.visualization import sinogramviewer
 
 logging.disable(logging.INFO)
@@ -53,7 +53,7 @@ class TestSinogramViewer(TestCaseQt):
         self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
 
         self.tmp_dir = tempfile.mkdtemp()
-        self.scan = MockHDF5(
+        self.scan = MockNXtomo(
             scan_path=os.path.join(self.tmp_dir, "myscan"),
             n_proj=20,
             n_ini_proj=20,

tomwer/gui/visualization/test/test_stacks.py

@@ -39,7 +39,7 @@ from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
 from tomoscan.esrf.volume.edfvolume import EDFVolume
 
-from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.core.utils.scanutils import MockNXtomo
 from tomwer.gui.stacks import RadioStack, SliceStack
 from tomwer.tests.utils import skip_gui_test
 
@@ -67,7 +67,7 @@ class TestSliceStack(TestCaseQt):
         n_slice_per_scan = 1
         with tempfile.TemporaryDirectory() as root_dir:
             for i_scan in range(n_scan):
-                scan = MockHDF5(
+                scan = MockNXtomo(
                     scan_path=os.path.join(root_dir, f"scan{i_scan}"),
                     n_proj=10,
                     n_ini_proj=10,
@@ -103,7 +103,7 @@ class TestRadioStack(TestCaseQt):
         self.slider = weakref.ref(self._widget._viewer._qslider)
         self._tmp_dir = tempfile.mkdtemp()
         os.makedirs(self._tmp_dir, exist_ok=True)
-        self._scan = MockHDF5(
+        self._scan = MockNXtomo(
             os.path.join(self._tmp_dir, "my_scan"),
             n_proj=30,
             dim=10,

tomwer/gui/visualization/test/test_volumeviewer.py

@@ -1,84 +1,82 @@
-# 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.
-#
-#############################################################################*/
-
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "21/06/2021"
-
-
 import logging
 import os
-import shutil
-import tempfile
-import unittest
-
+import pytest
 import numpy
+from time import sleep
+
 from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
 from tomoscan.esrf.volume.hdf5volume import HDF5Volume
+from tomoscan.esrf.volume.tiffvolume import TIFFVolume, has_tifffile
 
-from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.tests.conftest import qtapp  # noqa F401
+from tomwer.core.utils.scanutils import MockNXtomo
 from tomwer.gui.visualization.volumeviewer import VolumeViewer
 
 logging.disable(logging.INFO)
 
 
-class TestDiffViewer(TestCaseQt):
-    """unit test for the :class:_ImageStack widget"""
+@pytest.mark.skipif(not has_tifffile, reason="tifffile not available")
+def test_volume_viewer(
+    qtapp,  # noqa F811
+    tmp_path,
+):
+    """
+    test the volume viewer setting a scan having an HDF5 volume linked to it
+    """
+
+    widget = VolumeViewer(parent=None)
+    widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+
+    tmp_dir = tmp_path / "test_volume_viewer"
+    tmp_dir.mkdir()
+
+    # step 1 - test setting a scan containing a HDF5Volume
+    scan = MockNXtomo(
+        scan_path=os.path.join(str(tmp_dir), "myscan"),
+        n_proj=20,
+        n_ini_proj=20,
+        dim=10,
+    ).scan
+    volume = HDF5Volume(
+        file_path=os.path.join(scan.path, "volume.hdf5"),
+        data_path="entry",
+        data=numpy.random.random(60 * 10 * 10).reshape(60, 10, 10),
+    )
+    volume.save()
 
-    def setUp(self):
-        TestCaseQt.setUp(self)
-        self._widget = VolumeViewer(parent=None)
-        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+    scan.set_latest_vol_reconstructions(
+        [
+            volume,
+        ]
+    )
 
-        self.tmp_dir = tempfile.mkdtemp()
+    widget.setScan(scan)
+    assert widget._centralWidget.data() is not None
+    widget.clear()
+    assert widget._centralWidget.data() is None
 
-        self.scan = MockHDF5(
-            scan_path=os.path.join(self.tmp_dir, "myscan"),
-            n_proj=20,
-            n_ini_proj=20,
-            dim=10,
-        ).scan
-        volume = HDF5Volume(
-            file_path=os.path.join(self.scan.path, "volume.hdf5"),
-            data_path="entry",
-            data=numpy.random.random(60 * 10 * 10).reshape(60, 10, 10),
-        )
-        volume.save()
+    # step 2: test setting a a tiff volume dirrectly
+    volume = TIFFVolume(
+        folder=os.path.join(tmp_dir, "my_tiff_vol"),
+        data=numpy.random.random(60 * 100 * 100).reshape(60, 100, 100),
+    )
+    volume.save()
 
-        self.scan.set_latest_vol_reconstructions(
-            [
-                volume,
-            ]
-        )
+    # 2.1 test with the data being in cache
+    widget.setVolume(volume=volume)
+    assert widget._centralWidget.data() is not None
+    widget.clear()
+    assert widget._centralWidget.data() is None
 
-    def tearDown(self):
-        shutil.rmtree(self.tmp_dir)
-        self._widget.close()
-        self._widget = None
-        unittest.TestCase.tearDown(self)
+    # 2.2 test with the data not being in cache anymore
+    volume.clear_cache()
 
-    def test(self):
-        self._widget.setScan(self.scan)
+    widget.setVolume(volume=volume)
+    # wait_for_processing_finished
+    while qt.QApplication.instance().hasPendingEvents():
+        qt.QApplication.instance().processEvents()
+    sleep(1.2)  # wait for the thread to be processed
+    while qt.QApplication.instance().hasPendingEvents():
+        qt.QApplication.instance().processEvents()
+    # end waiting
+    assert widget._centralWidget.data() is not None