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

orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -41,9 +41,9 @@ from silx.gui import qt
 import tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
-from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.sadeltabeta import SADeltaBetaTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.gui.reconstruction.sadeltabeta import (
@@ -198,16 +198,14 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     Details about :ref:`sadeltabeta score calculation`
     """
 
-    name = "semi automatic delta/beta calculation"
+    name = "multi-pag (sa-delta/beta calculation)"
     id = "orange.widgets.tomwer.sa_delta_beta"
-    description = (
-        "compute several delta / beta value to get the optimal "
-        "delta / beta value (before reconstructing a volume for "
-        "example."
-    )
+    description = "Reconstruct a slice with several delta / beta values."
     icon = "icons/delta_beta_range.png"
     priority = 22
     keywords = [
+        "multi",
+        "multi-pag",
         "tomography",
         "semi automatic",
         "half automatic",
@@ -257,12 +255,6 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     class Outputs:
         data = Output(name="data", type=TomwerScanBase)
 
-        future_out = Output(
-            name="future_tomo_obj",
-            type=FutureTomwerObject,
-            doc="data with some remote processing",
-        )
-
     def __init__(self, parent=None):
         """
 
@@ -285,7 +277,6 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
 
         # connect signal / slot
         self._widget.sigConfigurationChanged.connect(self._updateSettings)
-        self.destroyed.connect(self._widget.stop)
         self._widget._processing_stack.sigComputationStarted.connect(
             self._startProcessing
         )
@@ -336,9 +327,7 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             scan.sa_delta_beta_params = QSADeltaBetaParams()
         self._skipCurrentScan(new_scan=scan)
 
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             self.notify_skip(
                 scan=scan,
                 details=f"sa-delta-beta has been skiped for {scan} because of low space in lbsram",
@@ -393,14 +382,6 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             "autofocus_lock": self._widget.isAutoFocusLock(),
         }
 
-    def close(self):
-        self.stop()
-        self._widget = None
-        super().close()
-
-    def stop(self):
-        self._widget.stop()
-
     def getConfiguration(self):
         return self._widget.getConfiguration()
 
@@ -418,3 +399,14 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             # if possible process next
             if self._widget._processing_stack.can_process_next():
                 self._widget._processing_stack._process_next()
+
+    def getWaitingOverlay(self):
+        return self._widget._tabWidget._resultsViewer._plot.getWaiterOverlay()
+
+    def _startProcessing(self, *args, **kwargs):
+        self.getWaitingOverlay().show()
+        super()._startProcessing()
+
+    def _endProcessing(self, *args, **kwargs):
+        self.getWaitingOverlay().hide()
+        super()._endProcessing()

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

@@ -42,7 +42,8 @@ from tomoscan.normalization import Method as NormMethod
 
 from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
 from tomwer.core.process.reconstruction.normalization.params import _ValueSource
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -163,7 +164,6 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
 
         # connect signal / slot
         self._window.sigConfigurationChanged.connect(self._updateSettings)
-        self.destroyed.connect(self._window.stop)
         self._window._processing_stack.sigComputationStarted.connect(
             self._startProcessing
         )
@@ -197,9 +197,7 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
             return
 
         self._skipCurrentScan(new_scan=scan)
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             details = f"skip {scan} because low memory on lbsram"
             self.notify_skip(scan=scan, details=details)
             self.Outputs.data_out.send(scan)
@@ -219,17 +217,18 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
         tomwer_processing_res_code = extra_infos.pop(
             "tomwer_processing_res_code", "unprocessed"
         )
-        SinoNormalizationTask._register_process(
-            process_file=scan.process_file,
-            process=SinoNormalizationTask,
-            entry=scan.entry,
-            configuration=self.getConfiguration(),
-            results={
-                "method": scan.intensity_normalization.method.value,
-                "extra_infos": extra_infos,
-            },
-            process_index=scan.pop_process_index(),
-        )
+        with scan.acquire_process_file_lock():
+            SinoNormalizationTask._register_process(
+                process_file=scan.process_file,
+                process=SinoNormalizationTask,
+                entry=scan.entry,
+                configuration=self.getConfiguration(),
+                results={
+                    "method": scan.intensity_normalization.method.value,
+                    "extra_infos": extra_infos,
+                },
+                process_index=scan.pop_process_index(),
+            )
         if tomwer_processing_res_code is True:
             # if defined by manual scalar we need to set the value
             if extra_infos.get("source", None) == _ValueSource.MANUAL_SCALAR.value:
@@ -293,9 +292,6 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
     def getConfiguration(self):
         return self._window.getConfiguration()
 
-    def stop(self):
-        self._window.stop()
-
     def _updateSettings(self):
         self._ewoks_default_inputs = self._window.getConfiguration()
         self._ewoks_default_inputs["__lock__"] = self.isLocked()

orangecontrib/tomwer/widgets/visualization/DataViewerOW.py

@@ -120,15 +120,15 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         return qt.QSize(400, 500)
 
     def _updateSettings(self):
-        self._viewer_config[  # pylint: disable=E1137
-            "mode"
-        ] = self.viewer.getDisplayMode().value
-        self._viewer_config[  # pylint: disable=E1137
-            "slice_opt"
-        ] = self.viewer.getSliceOption().value
-        self._viewer_config[  # pylint: disable=E1137
-            "radio_opt"
-        ] = self.viewer.getRadioOption().value
+        self._viewer_config["mode"] = (  # pylint: disable=E1137
+            self.viewer.getDisplayMode().value
+        )
+        self._viewer_config["slice_opt"] = (  # pylint: disable=E1137
+            self.viewer.getSliceOption().value
+        )
+        self._viewer_config["radio_opt"] = (  # pylint: disable=E1137
+            self.viewer.getRadioOption().value
+        )
 
     def _setSettings(self, settings):
         old_state = self.viewer.blockSignals(True)

orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py

@@ -47,7 +47,7 @@ class DiffViewerOW(widget.OWBaseWidget, openclass=True):
     Allows to compare two random frame.
     """
 
-    name = "diff viewer"
+    name = "diff frame viewer"
     id = "orangecontrib.tomwer.widgets.visualization.diffviewerow"
     description = "Allows comparison between two random frame from a scan"
     icon = "icons/diff.png"

orangecontrib/tomwer/widgets/visualization/LivesliceOW.py

@@ -32,7 +32,7 @@ from orangewidget.widget import Input
 
 import tomwer.core.process.visualization.liveslice
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.utils import getFirstProjFile
+from tomwer.core.utils.spec import getFirstProjFile
 
 try:
     from liveslice.gui.liveslice_gui import ReconstructionApp

orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py

@@ -2,7 +2,7 @@ from orangewidget import gui, widget
 from orangewidget.widget import Input, Output
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
 
@@ -56,9 +56,9 @@ class NXtomoMetadataViewerOW(widget.OWBaseWidget, openclass=True):
     def setScan(self, scan):
         if scan is None:
             pass
-        elif not isinstance(scan, HDF5TomoScan):
+        elif not isinstance(scan, NXtomoScan):
             raise TypeError(
-                f"expect to have an instance of {HDF5TomoScan}. {type(scan)} provided."
+                f"expect to have an instance of {NXtomoScan}. {type(scan)} provided."
             )
         else:
             self.widget.setScan(scan)

orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py

@@ -79,7 +79,6 @@ class SinogramViewerOW(WidgetLongProcessing, widget.OWBaseWidget, openclass=True
         # connect signal / slot
         self._viewer.sigSinoLoadStarted.connect(self._startProcessing)
         self._viewer.sigSinoLoadEnded.connect(self._endProcessing)
-        self.destroyed.connect(self._viewer._stopAnimationThread)
 
     @Inputs.data
     def addLeafScan(self, scanID):

orangecontrib/tomwer/widgets/visualization/VolumeViewerOW.py

@@ -1,32 +1,3 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 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.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "21/07/2020"
-
 import pytest
 from orangewidget import gui, widget
 from orangewidget.widget import Input
@@ -79,6 +50,9 @@ class VolumeViewerOW(widget.OWBaseWidget, openclass=True):
         self.viewer.setScan(scan)
 
     @Inputs.volume
+    def _volumeReceived(self, volume, *args, **kwargs):
+        self.addVolume(volume)
+
     def addVolume(self, volume):
         if volume is None:
             return

tomwer/__main__.py

@@ -36,21 +36,16 @@ __date__ = "10/11/2020"
 
 
 import sys
-import logging
-import traceback
 from collections import namedtuple
 import tomwer.version
 from tomwer.utils import Launcher as _Launcher
-
+from tomwer.core.utils.deprecation import deprecated_warning
 
 DeprecationWarning = namedtuple(
     "DeprecationWarning", ["since", "reason", "replacement"]
 )
 
 
-depreclog = logging.getLogger("nxtomomill.DEPRECATION")
-
-
 class Launcher(_Launcher):
     """
     Manage launch of module.
@@ -115,48 +110,6 @@ class Launcher(_Launcher):
         super().execute(argv=argv)
 
 
-def deprecated_warning(
-    type_,
-    name,
-    reason=None,
-    replacement=None,
-    since_version=None,
-    skip_backtrace_count=0,
-):
-    """
-    Function to log a deprecation warning
-
-    :param str type_: Nature of the object to be deprecated:
-        "Module", "Function", "Class" ...
-    :param name: Object name.
-    :param str reason: Reason for deprecating this function
-        (e.g. "feature no longer provided",
-    :param str replacement: Name of replacement function (if the reason for
-        deprecating was to rename the function)
-    :param str since_version: First *silx* version for which the function was
-        deprecated (e.g. "0.5.0").
-    :param int skip_backtrace_count: Amount of last backtrace to ignore when
-        logging the backtrace
-    """
-    if not depreclog.isEnabledFor(logging.WARNING):
-        # Avoid computation when it is not logged
-        return
-
-    msg = "%s %s is deprecated"
-    if since_version is not None:
-        msg += " since silx version %s" % since_version
-    msg += "."
-    if reason is not None:
-        msg += " Reason: %s." % reason
-    if replacement is not None:
-        msg += " Use '%s' instead." % replacement
-    msg += "\n%s"
-    limit = 2 + skip_backtrace_count
-    backtrace = "".join(traceback.format_stack(limit=limit)[0])
-    backtrace = backtrace.rstrip()
-    depreclog.warning(msg, type_, name, backtrace)
-
-
 def main():
     """Main function of the launcher
 
@@ -216,14 +169,14 @@ def main():
         description="Tool to compute intensity normalization.",
     )
     launcher.add_command(
-        "lamino",
-        module_name="tomwer.app.lamino",
-        description="Run laminography reconstruction using tofu",
+        "multi-cor",
+        module_name="tomwer.app.multicor",
+        description="Compute a slice with different values of cor",
     )
     launcher.add_command(
-        "liveslice",
-        module_name="tomwer.app.liveslice",
-        description="Run liveslice application",
+        "multi-pag",
+        module_name="tomwer.app.multipag",
+        description="compute a slice with different values of delta / beta values",
     )
     launcher.add_command(
         "nabu",
@@ -273,16 +226,6 @@ def main():
         module_name="tomwer.app.sinogramviewer",
         description="Allows to compute on the fly sinogram " "and display them",
     )
-    launcher.add_command(
-        "sa-axis",
-        module_name="tomwer.app.saaxis",
-        description="Semi-automatic center of rotation research",
-    )
-    launcher.add_command(
-        "sa-delta-beta",
-        module_name="tomwer.app.sadeltabeta",
-        description="Semi-automatic delta/beta Paganin parameter research",
-    )
     launcher.add_command(
         "scan-viewer",
         module_name="tomwer.app.scanviewer",

tomwer/app/axis.py

@@ -6,7 +6,7 @@ import functools
 import logging
 import signal
 import sys
-
+import silx
 from silx.gui import qt
 
 from tomwer.core.process.reconstruction.axis.axis import (
@@ -124,9 +124,9 @@ def main(argv):
         logging.root.setLevel(logging.DEBUG)
 
     if options.use_opengl_plot:
-        import silx
-
         silx.config.DEFAULT_PLOT_BACKEND = "gl"
+    else:
+        silx.config.DEFAULT_PLOT_BACKEND = "matplotlib"
 
     increase_max_number_file()
 

tomwer/app/canvas.py

@@ -23,11 +23,19 @@ except ImportError:
     has_nabu = False
 else:
     has_nabu = True
+try:
+    import nxtomo.version
+except ImportError:
+    has_nxtomo = False
+else:
+    has_nxtomo = True
 
 
 def print_versions():
     print(f"tomwer version is {tomwer.version.version}")
     print(f"tomoscan version is {tomoscan.version.version}")
+    if has_nxtomo:
+        print(f"nxtomo version is {nxtomo.version.version}")
     if has_nxtomomill:
         print(f"nxtomomill version is {nxtomomill.version.version}")
     if has_nabu:

tomwer/app/canvas_launcher/config.py

@@ -112,9 +112,9 @@ class TomwerConfig(config.Config):
 
         all_eps = sorted(
             all_eps,
-            key=lambda ep: 0
-            if ep.dist.project_name.lower() in ("orange3", "tomwer")
-            else 1,
+            key=lambda ep: (
+                0 if ep.dist.project_name.lower() in ("orange3", "tomwer") else 1
+            ),
         )
         return iter(all_eps)
 
@@ -185,17 +185,19 @@ class TerminalTextDocument(_TerminalTextDocument):
     def writeWithFormat(self, string: str, charformat) -> None:
         assert qt.QThread.currentThread() is self.thread()
         # remove linux reset sequence
-        string = string.replace("\033[0m", "")
-        # remove linux reset sequence
-        string = string.replace("\033[1;%dm", "")
-        # remove linux reset sequence
-        string = string.replace("\x1B[1m", "")
-        string = string.replace("\x1B[1;30m", "")
-        string = string.replace("\x1B[1;31m", "")
-        string = string.replace("\x1B[1;32m", "")
-        string = string.replace("\x1B[1;33m", "")
-        string = string.replace("\x1B[1;34m", "")
-        string = string.replace("\x1B[1;35m", "")
+        from tomwer.core.log import logger as tomwer_logger
+
+        for sequence in (
+            tomwer_logger._RESET_SEQ,
+            tomwer_logger._BOLD_SEQ,
+            tomwer_logger._BLACK,
+            tomwer_logger._RED,
+            tomwer_logger._GREEN,
+            tomwer_logger._YELLOW,
+            tomwer_logger._BLUE,
+            tomwer_logger._MAGENTA,
+        ):
+            string = string.replace(sequence, "")
 
         color = self.get_log_level(string) or qt.Qt.red
         charformat.setForeground(color)

tomwer/app/canvas_launcher/environ.py

@@ -40,6 +40,7 @@ orangerc.cfg
     canvas_settings_dir = %(prefix)s/config/%(name)s/canvas
 
 """
+
 import configparser
 import os
 import sys

tomwer/app/canvas_launcher/mainwindow.py

@@ -4,6 +4,7 @@ import os
 import shutil
 import signal
 import sys
+import silx
 from typing import List
 from contextlib import closing
 from logging.handlers import RotatingFileHandler
@@ -299,13 +300,15 @@ class _OMain(ocMain):
         # define an environment variable.
         # this way we should also be able to let the user define it
         # on it's own later...
+
         if self.options.use_opengl_plot:
-            import silx
 
             # other standalones are not passing by the silx.config
             # but for the canvas this is way simpler to use it.
             # then all plot which have backend==None will pick the default plot backend
             silx.config.DEFAULT_PLOT_BACKEND = "gl"
+        else:
+            silx.config.DEFAULT_PLOT_BACKEND = "matplotlib"
 
     def setup_logging(self):
         super().setup_logging()

tomwer/app/darkref.py

@@ -1,4 +1,4 @@
-from silx.utils.deprecation import deprecated_warning
+from tomwer.core.utils.deprecation import deprecated_warning
 
 deprecated_warning(
     "module",

tomwer/app/darkrefpatch.py

@@ -1,4 +1,4 @@
-from silx.utils.deprecation import deprecated_warning
+from tomwer.core.utils.deprecation import deprecated_warning
 
 deprecated_warning(
     "module",

tomwer/app/diffframe.py

@@ -5,7 +5,7 @@ import argparse
 import logging
 import signal
 import sys
-
+import silx
 from silx.gui import qt
 
 from tomwer.core.scan.scanfactory import ScanFactory
@@ -82,9 +82,9 @@ def main(argv):
         scan_2 = None
 
     if options.use_opengl_plot:
-        import silx
-
         silx.config.DEFAULT_PLOT_BACKEND = "gl"
+    else:
+        silx.config.DEFAULT_PLOT_BACKEND = "matplotlib"
 
     # handle gui
     widget = DiffFrameViewer(parent=None)

tomwer/app/imagekeyeditor.py

@@ -8,7 +8,7 @@ import sys
 
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.core.process.edit.imagekeyeditor import ImageKeyEditorTask
 from tomwer.gui import icons
@@ -25,8 +25,8 @@ class ImageKeyDialog(_ImageKeyDialog):
         self._scan = None
 
     def setScan(self, scan):
-        if not isinstance(scan, HDF5TomoScan):
-            raise TypeError("This only manage HDF5TomoScan")
+        if not isinstance(scan, NXtomoScan):
+            raise TypeError("This only manage NXtomoScan")
         self._scan = scan
         _ImageKeyDialog.setScan(self, scan)
 
@@ -65,8 +65,8 @@ def main(argv):
     parser.add_argument("entry", default=None, help="Entry to treat")
     options = parser.parse_args(argv[1:])
 
-    # image key can only handle HDF5Tomoscan for now
-    scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+    # image key can only handle NXtomoScan for now
+    scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     increase_max_number_file()
 
     app = qt.QApplication.instance() or qt.QApplication(["tomwer"])

tomwer/app/imagekeyupgrader.py

@@ -9,7 +9,7 @@ import sys
 from silx.gui import qt
 
 from tomwer.core.process.edit.imagekeyeditor import ImageKeyUpgraderTask
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.edit.imagekeyeditor import (
@@ -40,8 +40,8 @@ class ImageKeyUpgraderDialog(qt.QDialog):
         self._buttons.button(qt.QDialogButtonBox.Cancel).released.connect(self.close)
 
     def setScan(self, scan):
-        if not isinstance(scan, HDF5TomoScan):
-            raise TypeError("This only manage HDF5TomoScan")
+        if not isinstance(scan, NXtomoScan):
+            raise TypeError("This only manage NXtomoScan")
         self._scan = scan
 
     def validate(self):
@@ -74,8 +74,8 @@ def main(argv):
     parser.add_argument("entry", default=None, help="Entry to treat")
     options = parser.parse_args(argv[1:])
 
-    # image key can only handle HDF5Tomoscan for now
-    scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+    # image key can only handle NXtomoScan for now
+    scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     increase_max_number_file()
 
     app = qt.QApplication.instance() or qt.QApplication(["tomwer"])

tomwer/app/intensitynormalization.py

@@ -10,7 +10,7 @@ import sys
 from silx.gui import qt
 
 from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
-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.gui import icons
@@ -72,17 +72,18 @@ class NormIntensityWindow(_SinoNormWindow):
     def _validated(self):
         scan = self.getScan()
         if scan is not None:
-            SinoNormalizationTask._register_process(
-                process_file=scan.process_file,
-                process=SinoNormalizationTask,
-                entry=scan.entry,
-                configuration=self.getConfiguration(),
-                results={
-                    "method": scan.intensity_normalization.method.value,
-                    "extra_infos": scan.intensity_normalization.get_extra_infos(),
-                },
-                process_index=scan.pop_process_index(),
-            )
+            with scan.acquire_process_file_lock():
+                SinoNormalizationTask._register_process(
+                    process_file=scan.process_file,
+                    process=SinoNormalizationTask,
+                    entry=scan.entry,
+                    configuration=self.getConfiguration(),
+                    results={
+                        "method": scan.intensity_normalization.method.value,
+                        "extra_infos": scan.intensity_normalization.get_extra_infos(),
+                    },
+                    process_index=scan.pop_process_index(),
+                )
         self.close()
 
     def _launchProcessing(self):
@@ -175,7 +176,7 @@ def main(argv):
                 )
             if options.entry is None:
                 raise ValueError("entry in the master file should be specify")
-            scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+            scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     else:
         scan = ScanFactory.mock_scan()
     # define the process_index is any tomwer_processes_existing