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

tomwer/synctools/axis.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "03/05/2019"
-
+from __future__ import annotations
 
 import logging
 

tomwer/synctools/darkref.py

@@ -1,30 +1,5 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "03/05/2019"
+from __future__ import annotations
 
 
 import logging

tomwer/synctools/datalistener.py

@@ -1,31 +1,5 @@
 # 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__ = "16/03/2020"
+from __future__ import annotations
 
 
 import logging

tomwer/synctools/datatransfert.py

@@ -1,31 +1,5 @@
 # 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__ = "28/01/2019"
+from __future__ import annotations
 
 
 from silx.gui import qt
@@ -38,6 +12,7 @@ from tomwer.core.scan.scanbase import TomwerScanBase
 
 class ScanTransfer(qt.QObject, FolderTransfertP):
     scanready = qt.Signal(TomwerScanBase)
+    """emit when scan ready"""
 
     def __init__(self, parent=None, inputs=None, varinfo=None):
         qt.QObject.__init__(self, parent)

tomwer/synctools/imageloaderthread.py

@@ -1,32 +1,5 @@
-# /*##########################################################################
-# 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.
-#
-#############################################################################*/
+from __future__ import annotations
 
-__author__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "02/06/2017"
 
 import logging
 import os

tomwer/synctools/rsyncmanager.py

@@ -1,34 +1,10 @@
 # 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.
-#
-#############################################################################*/
 
 """
 This module is used to manage the rsync between files for transfert.
 """
 
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "11/04/2017"
+from __future__ import annotations
 
 
 import logging

tomwer/synctools/saaxis.py

@@ -1,31 +1,6 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "03/05/2019"
 
+from __future__ import annotations
 
 import logging
 

tomwer/synctools/sadeltabeta.py

@@ -1,31 +1,6 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "20/05/2021"
 
+from __future__ import annotations
 
 import logging
 

tomwer/synctools/stacks/control/datalistener.py

@@ -1,30 +1,5 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "16/11/2020"
+from __future__ import annotations
 
 
 from silx.gui import qt

tomwer/synctools/stacks/processingstack.py

@@ -1,35 +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.
-#
-#############################################################################
 """Define some processing stack"""
 
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "08/01/2020"
-
+from __future__ import annotations
 
 from collections import deque
-from typing import Optional
 from tomwer.core.tomwer_object import TomwerObject
 from silx.gui.utils import blockSignals
 
@@ -68,14 +41,14 @@ class FIFO(SuperviseProcess):
         self._processing = False
 
     @property
-    def data_currently_computed(self) -> Optional[TomwerObject]:
+    def data_currently_computed(self) -> TomwerObject | None:
         return self._data_currently_computed
 
     def add(self, data, configuration=None, callback=None):
         """
         add a scan to process
 
-        :param TomwerScanBase scan: scan to process
+        :param data: data to process
         :param configuration: configuration of the process
         :param callback: function to call once the processing is Done
         """
@@ -106,9 +79,7 @@ class FIFO(SuperviseProcess):
 
     def can_process_next(self):
         """
-        :return: True if the computation thread is ready to compute
-        a new axis position
-        :rtype: bool
+        :return: True if the computation thread is ready to compute a new axis position
         """
         return not self._processing
 

tomwer/synctools/stacks/reconstruction/axis.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "03/05/2019"
-
+from __future__ import annotations
 
 import functools
 import logging
@@ -49,7 +23,7 @@ _logger = logging.getLogger(__name__)
 
 
 class AxisProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisProcess` but having a stack for treating
+    """Implementation of the `.AxisTask` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, axis_params, process_id=None):
@@ -81,10 +55,7 @@ class AxisProcessStack(FIFO, qt.QObject):
             if callback is not None:
                 callback()
             self.scan_ready(scan=data)
-        elif not self._axis_params.use_sinogram and mode in (
-            AxisMode.manual,
-            AxisMode.read,
-        ):
+        elif mode is (AxisMode.manual,):
             # if cor is not set then set it to 0 (can be the case if no)
             # interaction has been dne
             cor = self._axis_params.relative_cor_value
@@ -113,14 +84,6 @@ class AxisProcessStack(FIFO, qt.QObject):
             # we will keep the actual one (should have been defined previously)
             self._end_computation(data=data, future_tomo_obj=None, callback=callback)
 
-        elif (
-            not self._axis_params.use_sinogram
-            and mode not in AxisTask._CALCULATIONS_METHODS
-        ):
-            _logger.warning(f"no method defined to compute {mode}")
-            if callback is not None:
-                callback()
-            self._process_next()
         else:
             _logger.processStarted(
                 f"Start cor calculation on {data} ({self._axis_params.get_simple_str()})"
@@ -142,7 +105,7 @@ class AxisProcessStack(FIFO, qt.QObject):
         """
         assert isinstance(data, TomwerScanBase)
         assert self._axis_params is not None
-        # copy result computed on scan on the AxisProcess reconsparams
+        # copy result computed on scan on the AxisTask reconsparams
         self._axis_params.set_relative_value(
             data.axis_params.relative_cor_value
         )  # noqa
@@ -196,23 +159,13 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
             },
             process_id=self.process_id,
         )
-        axis = self.apply_patch(axis=axis)
         try:
             axis.run()
         except NoAxisUrl as e:
             self.center_of_rotation = None
-            _logger.error(str(e))
+            _logger.error(f"CoR calculation failed. Issue with input ({e})")
         except Exception as e:
-            _logger.error(str(e))
+            _logger.error(f"CoR calculation failed ({e})", stack_info=True)
             self.center_of_rotation = None
         else:
             self.center_of_rotation = self._scan.axis_params.relative_cor_value
-
-    def patch_calc_method(self, mode, function):
-        self.__patch[mode] = function
-
-    def apply_patch(self, axis):
-        for mode, patch_fct in self.__patch.items():
-            if mode in AxisMode:
-                axis._CALCULATIONS_METHODS[mode] = patch_fct
-        return axis

tomwer/synctools/stacks/reconstruction/castvolume.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "15/21/2021"
-
+from __future__ import annotations
 
 import functools
 import logging
@@ -86,12 +60,12 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip volume cast {data}"
             ProcessManager().notify_dataset_state(
-                dataset=data, process=self._process_id, state=DatasetState.SKIPPED
+                dataset=data, process=self, state=DatasetState.SKIPPED
             )
             _logger.processSkipped(mess)
             if callback is not None:
                 callback()
-            self.scan_ready(scan=data)
+                self._end_computation(data=data, future_tomo_obj=None, callback=None)
         else:
             self._data_currently_computed = data
             try:
@@ -101,12 +75,12 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
                 # then we want to keep the thread active
                 self._data_currently_computed = None
                 ProcessManager().notify_dataset_state(
-                    dataset=data, process=self._process_id, state=DatasetState.SKIPPED
+                    dataset=data, process=self, state=DatasetState.FAILED
                 )
-                _logger.processSkipped(f"thread initialization failed. Error is {e}")
+                _logger.processFailed(f"thread initialization failed. Error is {e}")
                 if callback is not None:
                     callback()
-                self.scan_ready(scan=data)
+                self._end_computation(data=data, future_tomo_obj=None, callback=None)
             else:
                 # need to manage connect before starting it because
                 fct_callback = functools.partial(
@@ -180,16 +154,17 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
 
     def run(self):
         self.sigComputationStarted.emit()
-        cast_volume = CastVolumeTask(
+        cast_volume_task = CastVolumeTask(
             process_id=self.process_id,
             varinfo=None,
             inputs={
                 "volume": self._volume,
                 "configuration": self._configuration,
+                "scan": self._scan,
             },
         )
         try:
-            cast_volume.run()
+            cast_volume_task.run()
         except Exception as e:
             _logger.error(str(e))
             if self._scan is not None:
@@ -201,12 +176,6 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
                 )
         else:
             if self._scan is not None:
-                # if scan is provided update status because otherwise only the volume state is updated
-                ProcessManager().notify_dataset_state(
-                    dataset=self._scan,
-                    process=self,
-                    state=DatasetState.SUCCEED,
-                )
-                self._scan.cast_volume = self._volume.cast_volume
-            if cast_volume.outputs.future_tomo_obj is not None:
-                self._future_tomo_obj = cast_volume.outputs.future_tomo_obj
+                self._scan.cast_volume = cast_volume_task.outputs.volume
+            if cast_volume_task.outputs.future_tomo_obj is not None:
+                self._future_tomo_obj = cast_volume_task.outputs.future_tomo_obj

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -1,30 +1,6 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016-2019 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__ = "13/08/2021"
+from __future__ import annotations
+
 
 import functools
 import logging
@@ -47,7 +23,7 @@ _logger = logging.getLogger(__name__)
 
 
 class DarkRefCopyProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisProcess` but having a stack for treating
+    """Implementation of the `.AxisTask` but having a stack for treating
     scans and making computation in threads"""
 
     sigRefSetted = qt.Signal(str)
@@ -183,6 +159,7 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
 
 class DarkRefsCopyWithSig(qt.QObject, DarkRefsCopy):
     sigRefSetted = qt.Signal(str)
+    """Signal emit when dark or flat are set by a scan. str is the scan identifier"""
 
     def __init__(self, parent=None, *args, **kwargs) -> None:
         qt.QObject.__init__(self, parent)