tomwer 1.2.0a1__py3-none-any.whl → 1.2.0a3__py3-none-any.whl

tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py

@@ -46,7 +46,7 @@ from tomwer.core.process.reconstruction.nabu.utils import (
     retrieve_lst_of_value_from_str,
 )
 from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
-    SADeltaBetaProcess,
+    SADeltaBetaTask,
 )
 from tomwer.core.process.reconstruction.scores.params import ScoreMethod
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -74,7 +74,7 @@ class ScorePlot(_ScorePlot, constructor=DelaBetaSelection):
             if scan.sa_delta_beta_params:
                 scan.sa_delta_beta_params.score_method = self.getScoreMethod()
                 # update autofocus
-                SADeltaBetaProcess.autofocus(scan)
+                SADeltaBetaTask.autofocus(scan)
         self.setVarScores(
             scores=self._scores,
             score_method=self.getScoreMethod(),
@@ -95,7 +95,7 @@ class _SADeltaBetaTabWidget(qt.QTabWidget):
     sigConfigurationChanged = qt.Signal()
     """Signal emit when the configuration changes"""
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, backend=None):
         qt.QTabWidget.__init__(self, parent=parent)
 
         self._deltaBetaSelectionWidget = DeltaBetaSelectionWidget(self)
@@ -111,7 +111,7 @@ class _SADeltaBetaTabWidget(qt.QTabWidget):
         nabu_icon = icons.getQIcon("nabu")
         self.addTab(self._nabuSettings, nabu_icon, "reconstruction settings")
         # results
-        self._resultsViewer = ScorePlot(self, variable_name="db")
+        self._resultsViewer = ScorePlot(self, variable_name="db", backend=backend)
         results_icon = icons.getQIcon("results")
         self.addTab(self._resultsViewer, results_icon, "reconstructed slices")
 
@@ -235,7 +235,7 @@ class SADeltaBetaWindow(qt.QMainWindow):
     Widget used to determine half-automatically the better delta / beta value
     """
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, backend=None):
         qt.QMainWindow.__init__(self, parent)
         self._db_values = []
         self._urls = []
@@ -248,7 +248,7 @@ class SADeltaBetaWindow(qt.QMainWindow):
         self._mainWidget.setLayout(qt.QVBoxLayout())
         self._scanInfo = ScanNameLabelAndShape(self)
         self._mainWidget.layout().addWidget(self._scanInfo)
-        self._tabWidget = _SADeltaBetaTabWidget(self)
+        self._tabWidget = _SADeltaBetaTabWidget(self, backend=backend)
         self._mainWidget.layout().addWidget(self._tabWidget)
         self.setCentralWidget(self._mainWidget)
         # next and previous buttons for browsing the tab widget

tomwer/gui/reconstruction/scores/scoreplot.py

@@ -64,8 +64,8 @@ class VariableScorePlot(PlotWidget):
 
     MARKER_COLOR = "#ff292199"
 
-    def __init__(self, parent):
-        PlotWidget.__init__(self, parent)
+    def __init__(self, parent, backend=None):
+        PlotWidget.__init__(self, parent, backend=backend)
         self._scores = {}
         self.setAxesDisplayed(False)
         self.setMaximumHeight(150)
@@ -293,6 +293,7 @@ class SingleValueSelection(VariableSelection):
 
 
 class DelaBetaSelection(SingleValueSelection):
+    # FIXME: fix typo Dela vs Delta
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         idx = self._scoreMethodCB.findText(ScoreMethod.TOMO_CONSISTENCY.value)
@@ -488,6 +489,7 @@ class ScorePlot(qt.QWidget):
         parent=None,
         variable_name=None,
         dims_colors=("#ffff5a", "#62efff", "#ff5bff"),
+        backend=None,
     ):
         if not isinstance(variable_name, str):
             raise TypeError("a variable name should be provided as a string")
@@ -500,7 +502,7 @@ class ScorePlot(qt.QWidget):
         # define GUI
         self.setLayout(qt.QGridLayout())
         # main plot
-        self._plot = ImageStack(self, show_overview=False)
+        self._plot = ImageStack(self, show_overview=False, backend=backend)
         self._plot.getPlotWidget().setYAxisInverted(settings.Y_AXIS_DOWNWARD)
 
         self._plot.getPlotWidget().setKeepDataAspectRatio(True)
@@ -878,7 +880,7 @@ class _VarSlider(qt.QWidget):
                 value = where[0]
                 if isinstance(value, numpy.ndarray):
                     value = value[0]
-                self._slider.setValue(value)
+                self._slider.setValue(int(value))
 
     def value(self):
         return self._slider.value()

tomwer/gui/samplemoved/__init__.py

@@ -70,14 +70,14 @@ class SampleMovedWidget(qt.QMainWindow):
     two projections
     """
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, backend=None):
         qt.QMainWindow.__init__(self, parent)
         self._scan = None
         self.setWindowFlags(qt.Qt.Widget)
         self._isConnected = False
         self._images = {}
         self._symmetricalStates = {"first": False, "second": False}
-        self._plot = CompareImages(parent=self)
+        self._plot = CompareImages(parent=self, backend=backend)
         self._plot.setWindowFlags(qt.Qt.Widget)
         self._plot.getPlot().setYAxisInverted(Y_AXIS_DOWNWARD)
         self._on_load_callback = []

tomwer/gui/stackplot.py

@@ -67,7 +67,7 @@ class _QImageStackPlot(qt.QWidget):
         )
     )
 
-    def __init__(self, parent, sliderVertical=False):
+    def __init__(self, parent, sliderVertical=False, backend=None):
         qt.QWidget.__init__(self, parent)
         self._transpose = False
         """If we want to transpose the image like imagj by default"""
@@ -82,7 +82,7 @@ class _QImageStackPlot(qt.QWidget):
         mainwidget.setLayout(mainLayout)
         layout.addWidget(mainwidget)
 
-        self._plot = Plot2D(self)
+        self._plot = Plot2D(self, backend=backend)
 
         def find_y_inverted(actions):
             for act in actions:
@@ -259,13 +259,15 @@ class _QImageFileStackPlot(_QImageStackPlot):
     file
     """
 
-    def __init__(self, parent):
+    def __init__(self, parent, backend=None):
         """
         Constructor
 
         :param parent: the Qt parent widget
         """
-        _QImageStackPlot.__init__(self, parent)
+        _QImageStackPlot.__init__(self, parent, backend=backend)
+        self._imagejThreads = []
+        # threads used to open frames with image j
 
         self._loadingMode = _LoadingModeToolButton(parent=self)
         self.getControlWidget().layout().addWidget(self._loadingMode)
@@ -393,7 +395,9 @@ class _QImageFileStackPlot(_QImageStackPlot):
             logger.warning("No active image defined")
         else:
             try:
-                utils.open_url_with_image_j(active_image.url)
+                self._imagejThreads.append(
+                    utils.open_url_with_image_j(active_image.url)
+                )
             except OSError as e:
                 msg = qt.QMessageBox(self)
                 msg.setIcon(qt.QMessageBox.Warning)
@@ -474,6 +478,10 @@ class _QImageFileStackPlot(_QImageStackPlot):
             self._qlFileName.setText("")
         super(_QImageFileStackPlot, self).clear()
 
+    def close(self):
+        [thread.quit() for thread in self._imagejThreads]
+        super.close()
+
 
 class _StackImage(object):
     def __init__(self, images: Optional[Iterable]):
@@ -601,8 +609,11 @@ class _StackImageToLoad(_StackImage, qt.QObject):
         return self._mode
 
     def _loadAllImages(self):
-        for imgIndex, img in self._images.items():
-            img.load_recons_params(self._force_sync)
+        for _, img in self._images.items():
+            try:
+                img.load(sync=self._force_sync)
+            except Exception as e:
+                logger.error(e)
 
     def _loaded(self, url_path):
         self.sigImageLoaded.emit(url_path)

tomwer/gui/stacks.py

@@ -67,11 +67,11 @@ class _ImageStack(qt.QMainWindow):
         copy.
     """
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, backend=None):
         qt.QMainWindow.__init__(self, parent)
         self.setWindowFlags(qt.Qt.Widget)
         self._scans = set()
-        self._viewer = _QImageFileStackPlot(parent=self)
+        self._viewer = _QImageFileStackPlot(parent=self, backend=backend)
         self._viewer.addFolderName(True)
         self.setCentralWidget(self._viewer)
 

tomwer/gui/stitching/stitchandbackground.py

@@ -38,13 +38,13 @@ class AlphaChannelWidget(qt.QWidget):
         self.sigAlphaBackgroundChanged.emit()
 
     def setAlphaStitchedImg(self, alpha: float):
-        self._alphaImgSlider.setValue(alpha * 100.0)
+        self._alphaImgSlider.setValue(int(alpha * 100.0))
 
     def getAlphaStitchedImg(self) -> float:
         return self._alphaImgSlider.value() / 100.0
 
     def setAlphaBackgroundImg(self, alpha: float):
-        self._alphaBackgroundSlider.setValue(alpha * 100.0)
+        self._alphaBackgroundSlider.setValue(int(alpha * 100.0))
 
     def getAlphaBackgroundImg(self) -> float:
         return self._alphaBackgroundSlider.value() / 100.0

tomwer/gui/stitching/stitching.py

@@ -703,7 +703,7 @@ class ZStitchingWindow(qt.QMainWindow):
             2: self._updateAxis2PosFromPreviewCalc.isChecked(),
         }
 
-        if update_requested[0] or update_requested[1]:
+        if update_requested[0] or update_requested[2]:
             existing_tomo_obj = {
                 tomo_obj.get_identifier().to_str(): tomo_obj
                 for tomo_obj in self._widget._mainWidget.getTomoObjs()

tomwer/gui/stitching/stitching_raw.py

@@ -572,4 +572,4 @@ class AlphaValueSlider(qt.QTableWidget):
         return self._slider.value()
 
     def setValue(self, value: int):
-        self._slider.setValue(value)
+        self._slider.setValue(int(value))

tomwer/gui/utils/__init__.py

@@ -1,85 +1 @@
-# coding: utf-8
-# /*##########################################################################
-# Copyright (C) 2017 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.
-#
-#############################################################################*/
-
-"""
-Some utils GUI associated to illustrations
-"""
-
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "29/01/2020"
-
-
-import logging
-import os
-import subprocess
-
-_logger = logging.getLogger(__name__)
-
-
-__has_image_j = None
-__image_j_from = None
-
-_IMAGE_J_BIN_PATH = "/sware/pub/ImageJ/ImageJ"
-
-
-def has_imagej():
-    """Return if imagej command is accessible from the computer"""
-    global __has_image_j
-    global __image_j_from
-    if __has_image_j is None:
-        try:
-            # use help because there is no information regarding version
-            subprocess.call(["imagej", "-h"], stdout=subprocess.PIPE)
-        except OSError:
-            if os.path.exists(_IMAGE_J_BIN_PATH):
-                __image_j_from = "binary"
-                __has_image_j = True
-            else:
-                __has_image_j = False
-        else:
-            __image_j_from = "command"
-            __has_image_j = True
-    return __has_image_j
-
-
-def open_url_with_image_j(url):
-    """open the url in an imagej subprocess
-
-    :param DataUrl url: url we want to open in imagej
-    """
-    global __image_j_from
-    if not has_imagej():
-        raise OSError("ImageJ is not installed")
-    elif __image_j_from == "command":
-        # for now we only manage the simple case of an edf file
-        try:
-            subprocess.call(["imagej", "-o", url.file_path()])
-        except Exception as e:
-            _logger.warning(f"Fail to open {url}. Reason is {e}")
-    elif __image_j_from == "binary":
-        try:
-            subprocess.call([_IMAGE_J_BIN_PATH, url.file_path()])
-        except Exception as e:
-            _logger.warning(f"Fail to open {url}. Reason is {e}")
+from .utils import has_imagej, open_url_with_image_j  # noqa F403

tomwer/gui/utils/illustrations.py

@@ -81,7 +81,7 @@ class _IllustrationWidget(qt.QWidget):
             height = event.size().height()
             width = self.widthForHeight(height)
 
-        self._display.resize(width, height)
+        self._display.resize(int(width), int(height))
         if self.isUsingSvg() is False:
             self._updatePixamp()
 

tomwer/gui/utils/inputwidget.py

@@ -28,7 +28,7 @@ __date__ = "16/08/2018"
 
 import logging
 import os
-from typing import Optional, Union
+from typing import Optional
 
 import numpy
 from nxtomomill.io.config import TomoEDFConfig as EDFConfig
@@ -41,6 +41,7 @@ from tomwer.gui import icons
 from tomwer.gui.qlefilesystem import QLFileSystem
 from tomwer.io.utils import get_default_directory
 from tomwer.core.volume.volumefactory import VolumeFactory
+from tomwer.core.process.control.nxtomomill import NXtomomillNXDefaultOutput
 
 from tomwer.core.volume import (
     EDFVolume,
@@ -71,11 +72,14 @@ class SelectionLineEdit(qt.QWidget):
 
     _DEFAULT_SELECTION = LIST_MODE
 
-    def __init__(self, text=None, parent=None):
+    def __init__(self, text=None, parent=None, allow_negative_indices=False):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QHBoxLayout())
         self._qLineEdit = qt.QLineEdit(parent=self)
-        fpm = "\\d*\\.?\\d+"  # float or int matching
+        if allow_negative_indices:
+            fpm = "\\-?\\d*\\.?\\d+"  # float or int matching
+        else:
+            fpm = "\\d*\\.?\\d+"  # float or int matching
         qRegExp = qt.QRegExp(
             "(" + fpm + "[;]?[,]?[ ]?){1,}" + "|" + ":".join((fpm, fpm, fpm))
         )
@@ -260,38 +264,33 @@ class NXTomomillOutputDirSelector(qt.QWidget):
     sigChanged = qt.Signal()
     """Signal emit when the output directory of the nx file change"""
 
-    DEFAULT_PROCESSED_DIR = (
-        "{scan_parent_dir_basename}/../../PROCESSED_DATA/{scan_dir_name}"
-    )
-    """Default pattern to find the 'processed' directory"""
-
     def __init__(self, parent=None):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
         self.__buttonGroup = qt.QButtonGroup(self)
         self.__buttonGroup.setExclusive(True)
 
-        tooltip = f"""Define the output directory of the nexus (.nx) file. Options are:
+        tooltip = """Define the output directory of the nexus (.nx) file. Options are:
         \n - next to bliss file: create the NXtomos at the same level as the bliss input file
-        \n - 'PROCESSED_DATA' folder: create NXtomos on the default 'PROCESSED_DATA' folder (bliss default folder, nearby the 'raw' folder). Uses {self.DEFAULT_PROCESSED_DIR} pattern
+        \n - 'PROCESSED_DATA' folder: create NXtomos on the default 'PROCESSED_DATA' folder (bliss default folder, nearby the 'raw' folder).
         \n - user defined folder: users can provide their own folders using keywords for string formatting such as 'scan_dir_name', 'scan_basename' or 'scan_parent_dir_basename'
         """
 
         # output dir is the folder containing the .nx file
-        self._closeToNxRB = qt.QRadioButton("next to bliss file", self)
-        self._closeToNxRB.setToolTip(tooltip)
-        self.layout().addWidget(self._closeToNxRB, 0, 0, 1, 1)
-        self.__buttonGroup.addButton(self._closeToNxRB)
+        self._closeToBlissFileRB = qt.QRadioButton("near input file", self)
+        self._closeToBlissFileRB.setToolTip(tooltip)
+        self.layout().addWidget(self._closeToBlissFileRB, 0, 0, 1, 1)
+        self.__buttonGroup.addButton(self._closeToBlissFileRB)
         # output dir is the default 'reduced'folder
-        self._processedFolderRB = qt.QRadioButton("'PROCESSED_DATA' folder", self)
-        self._processedFolderRB.setToolTip(tooltip)
-        self.layout().addWidget(self._processedFolderRB, 1, 0, 1, 1)
-        self.__buttonGroup.addButton(self._processedFolderRB)
+        self._processedDataFolderRB = qt.QRadioButton("'PROCESSED_DATA' folder", self)
+        self._processedDataFolderRB.setToolTip(tooltip)
+        self.layout().addWidget(self._processedDataFolderRB, 1, 0, 1, 1)
+        self.__buttonGroup.addButton(self._processedDataFolderRB)
         # manual
         self._manualRB = qt.QRadioButton("custom output directory", self)
         self._manualRB.setToolTip(tooltip)
         self.layout().addWidget(self._manualRB, 2, 0, 1, 1)
-        self._outputFolderQLE = qt.QLineEdit("", self)
+        self._outputFolderQLE = QLFileSystem("", self)
         self.layout().addWidget(self._outputFolderQLE, 2, 1, 1, 1)
         self._selectButton = qt.QPushButton("", self)
         style = qt.QApplication.style()
@@ -304,13 +303,13 @@ class NXTomomillOutputDirSelector(qt.QWidget):
         # connect signal / slot
         self._selectButton.released.connect(self._selectOutpuFolder)
         self.__buttonGroup.buttonReleased.connect(self._updateVisiblity)
-        self._closeToNxRB.toggled.connect(self._outputDirChanged)
-        self._processedFolderRB.toggled.connect(self._outputDirChanged)
+        self._closeToBlissFileRB.toggled.connect(self._outputDirChanged)
+        self._processedDataFolderRB.toggled.connect(self._outputDirChanged)
         self._manualRB.toggled.connect(self._outputDirChanged)
         self._outputFolderQLE.editingFinished.connect(self._outputDirChanged)
 
         # set up
-        self._closeToNxRB.setChecked(True)
+        self._processedDataFolderRB.setChecked(True)
         self._updateVisiblity()
 
     def _updateVisiblity(self, *args, **kwargs):
@@ -335,28 +334,34 @@ class NXTomomillOutputDirSelector(qt.QWidget):
         self._outputFolderQLE.setText(dialog.selectedFiles()[0])
         self.sigChanged.emit()
 
-    def getOutputFolder(self) -> Union[None, str]:
+    def getOutputFolder(self) -> str:
         if self._manualRB.isChecked():
             return self._outputFolderQLE.text()
-        elif self._processedFolderRB.isChecked():
-            return self.DEFAULT_PROCESSED_DIR
+        elif self._processedDataFolderRB.isChecked():
+            return NXtomomillNXDefaultOutput.PROCESSED_DATA.value
+        elif self._closeToBlissFileRB.isChecked():
+            return NXtomomillNXDefaultOutput.NEAR_INPUT_FILE.value
         else:
-            return None
+            raise RuntimeError("Use case - h52nx output dir - not handled")
 
-    def setOutputFolder(self, output_folder: Optional[str]):
+    def setOutputFolder(self, output_folder: str):
         old = self.blockSignals(True)
         self._manualRB.setChecked(output_folder is not None)
-        if output_folder is None:
-            self._closeToNxRB.setChecked(True)
+        try:
+            default_output = NXtomomillNXDefaultOutput.from_value(output_folder)
+        except ValueError:
+            self._outputFolderQLE.setText(output_folder)
+            self._manualRB.setChecked(True)
         else:
-            is_default_processed_folder = output_folder == self.DEFAULT_PROCESSED_DIR
-            if is_default_processed_folder:
-                self._processedFolderRB.setChecked(True)
+            if default_output is NXtomomillNXDefaultOutput.NEAR_INPUT_FILE:
+                self._processedDataFolderRB.setChecked(True)
+            elif default_output is NXtomomillNXDefaultOutput.PROCESSED_DATA:
+                self._closeToBlissFileRB.setChecked(True)
             else:
-                self._outputFolderQLE.setText(output_folder)
-                self._manualRB.setChecked(True)
-        self._updateVisiblity()
-        self.blockSignals(old)
+                raise ValueError(f"default output not handled ({default_output})")
+        finally:
+            self._updateVisiblity()
+            self.blockSignals(old)
 
 
 class _ConfigFileSelector(qt.QWidget):

tomwer/gui/utils/slider.py

@@ -73,7 +73,7 @@ class LogSlider(qt.QWidget):
         if min_ <= 0.0 or max_ <= 0.0:
             raise ValueError("LogSlider can only handled positive values")
         self._valueQBSB.setRange(min_, max_)
-        self._slider.setRange(numpy.log(min_), numpy.log(max_))
+        self._slider.setRange(int(numpy.log(min_)), int(numpy.log(max_)))
 
     def _sliderValueChanged(self, *args, **kwargs):
         old = self._valueQBSB.blockSignals(True)
@@ -83,7 +83,7 @@ class LogSlider(qt.QWidget):
 
     def _qdsbValueChanged(self, *args, **kwargs):
         old = self._slider.blockSignals(True)
-        self._slider.setValue(numpy.log(self._valueQBSB.value()))
+        self._slider.setValue(int(numpy.log(self._valueQBSB.value())))
         self._slider.blockSignals(old)
         self.valueChanged.emit(self.value())
 

tomwer/gui/utils/utils.py

@@ -0,0 +1,93 @@
+"""
+Some utils GUI associated to illustrations
+"""
+
+__authors__ = ["H.Payno"]
+__license__ = "MIT"
+__date__ = "29/01/2020"
+
+
+import logging
+import os
+import subprocess
+import threading
+import platform
+
+_logger = logging.getLogger(__name__)
+
+
+__has_image_j = None
+__image_j_from = None
+
+_IMAGE_J_BIN_PATH = "/sware/pub/ImageJ/ImageJ"
+
+
+def has_imagej():
+    """Return if imagej command is accessible from the computer"""
+    global __has_image_j
+    global __image_j_from
+    if __has_image_j is None:
+        if platform.machine() in ("x86_64", "AMD64") and os.path.exists(
+            _IMAGE_J_BIN_PATH
+        ):
+            __image_j_from = "binary"
+            __has_image_j = True
+        else:
+            try:
+                # use help because there is no information regarding version
+                subprocess.call(["imagej", "-h"], stdout=subprocess.PIPE)
+            except Exception:
+                __has_image_j = False
+            else:
+                __image_j_from = "command"
+                __has_image_j = True
+    return __has_image_j
+
+
+def open_url_with_image_j(url) -> threading.Thread:
+    """open the url in an imagej subprocess within a thread.
+    It is up to the caller to handle thread life
+
+    :param DataUrl url: url we want to open in imagej
+    """
+    global __image_j_from
+    if not has_imagej():
+        raise OSError("ImageJ is not installed")
+    thread = ImageJthread(url=url, image_j_from=__image_j_from)
+    thread.start()
+    return thread
+
+
+class ImageJthread(threading.Thread):
+    def __init__(self, url, image_j_from, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+        self._image_j_from = image_j_from
+        self._url = url
+        self._process = None
+
+    def run(self):
+        if self._image_j_from == "command":
+            # for now we only manage the simple case of an edf file
+            try:
+                self._process = subprocess.Popen(
+                    ["imagej", "-o", self._url.file_path()],
+                )
+            except Exception as e:
+                _logger.warning(f"Fail to open {self._url}. Reason is {e}")
+            else:
+                self._process.communicate()
+
+        elif self._image_j_from == "binary":
+            try:
+                self._process = subprocess.Popen(
+                    [_IMAGE_J_BIN_PATH, self._url.file_path()],
+                )
+            except Exception as e:
+                _logger.warning(f"Fail to open {self._url}. Reason is {e}")
+            else:
+                self._process.communicate()
+
+    def quit(self):
+        if self._process is not None:
+            self._process.kill()
+            self._process.wait()

tomwer/gui/visualization/dataviewer.py

@@ -77,12 +77,14 @@ class DataViewer(qt.QMainWindow):
     sigConfigChanged = qt.Signal()
     """Signal emitted when the settings (display mode, options...) changed. """
 
-    def __init__(self, parent, show_overview=True):
-        qt.QMainWindow.__init__(self, parent)
+    def __init__(self, parent, show_overview=True, backend=None):
+        super().__init__(parent)
         self.setWindowFlags(qt.Qt.Widget)
         self._scan = None
         # viewer
-        self._viewer = ImageStack(parent=self, show_overview=show_overview)
+        self._viewer = ImageStack(
+            parent=self, show_overview=show_overview, backend=backend
+        )
         self._viewer.getPlotWidget().setYAxisInverted(Y_AXIS_DOWNWARD)
         # set an UrlLoader managing .npy and .vol
         self._viewer.getPlotWidget().setKeepDataAspectRatio(True)
@@ -419,10 +421,11 @@ class DisplayControl(qt.QWidget):
 
 
 class ImageStack(_ImageStack):
-    def __init__(self, parent, show_overview=True):
+    def __init__(self, parent, show_overview=True, backend=None):
         self._normFct = None
         self._url_indexes = None
-        super(ImageStack, self).__init__(parent)
+        super().__init__(parent)
+        self.getPlotWidget().setBackend(backend)
         self.setUrlLoaderClass(_TomwerUrlLoader)
         # hide axis to be display
         self._plot.getPlotWidget().setAxesDisplayed(False)

tomwer/gui/visualization/diffviewer/diffviewer.py

@@ -57,8 +57,8 @@ _logger = logging.getLogger(__name__)
 
 
 class CompareImages(_CompareImages):
-    def __init__(self, parent=None):
-        super().__init__(parent=parent)
+    def __init__(self, parent=None, backend=None):
+        super().__init__(parent=parent, backend=backend)
         # ignore Pan with arrow keys. This should be used by the "arrowControlWidget"
         self.getPlot().setPanWithArrowKeys(False)
         self._firstVisible = True
@@ -371,7 +371,7 @@ class DiffFrameViewer(qt.QMainWindow):
     or dark.
     """
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, backend=None):
         qt.QMainWindow.__init__(self, parent)
         self.setWindowFlags(qt.Qt.Widget)
         # add frame selector
@@ -393,7 +393,7 @@ class DiffFrameViewer(qt.QMainWindow):
         self.addDockWidget(qt.Qt.TopDockWidgetArea, self._shiftDW)
 
         # define central widget
-        self._mainWidget = CompareImages(parent=self)
+        self._mainWidget = CompareImages(parent=self, backend=backend)
         self._mainWidget.setVisualizationMode(
             CompareImages.VisualizationMode.COMPOSITE_A_MINUS_B
         )