tomwer 1.0.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

tomwer/resources/gui/illustrations/ctf_z1.svg

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tomwer/synctools/datalistener.py

@@ -254,7 +254,11 @@ class MockDataListenerQThread(DataListenerQThread):
             current_acquisition.end(
                 end_time=now.strftime("%H:%M:%S"), succeed=True, error=None
             )
-            self._rpc_sequence_ended(acquisition=current_acquisition)
+            self._rpc_sequence_ended(
+                saving_file=current_acquisition.sample_file,
+                sequence_scan_number=current_acquisition.entry,
+                success=True,
+            )
             time.sleep(mock_acqui.waiting_time)
 
         # wait until stop the thread

tomwer/synctools/imageloaderthread.py

@@ -48,7 +48,7 @@ class ImageLoaderThread(qt.QThread):
         )
     )
 
-    def __init__(self, url):
+    def __init__(self, url, *args, **kwargs):
         """
 
         :param index: index of the image on the stackplot
@@ -57,7 +57,7 @@ class ImageLoaderThread(qt.QThread):
                          vol file then the name is given with the slice z index
                          to be loaded.
         """
-        super(qt.QThread, self).__init__()
+        super().__init__(*args, **kwargs)
         self.data = None
         self.url = url
 

tomwer/synctools/stacks/edit/imagekeyeditor.py

@@ -33,7 +33,7 @@ from tomwer.core.settings import get_lbsram_path, isOnLbsram
 from tomwer.core.utils import isLowOnMemory
 from ..processingstack import FIFO, ProcessingThread
 from tomwer.core.process.edit import imagekeyeditor
-from tomoscan.esrf.hdf5scan import ImageKey
+from tomoscan.esrf.scan.hdf5scan import ImageKey
 from processview.core.superviseprocess import SuperviseProcess
 from processview.core.manager import ProcessManager, DatasetState
 import logging

tomwer/synctools/stacks/processingstack.py

@@ -112,7 +112,7 @@ class FIFO(Queue, SuperviseProcess):
         """
         if callback is not None:
             callback()
-        sender = self.sender()
+        sender = self.sender()  # pylint: disable=E1101
         if hasattr(sender, "future_tomo_obj"):
             future_tomo_obj = sender.future_tomo_obj
         else:
@@ -142,7 +142,7 @@ class FIFO(Queue, SuperviseProcess):
         self.sigComputationStarted.emit(self._data_currently_computed)
 
     def _end_threaded_computation(self, callback=None):
-        sender = self.sender()
+        sender = self.sender()  # pylint: disable=E1101
         if hasattr(sender, "future_tomo_obj"):
             future_tomo_obj = sender.future_tomo_obj
         else:

tomwer/synctools/stacks/reconstruction/castvolume.py

@@ -189,5 +189,6 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
                     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

tomwer/synctools/stacks/reconstruction/lamino.py

@@ -38,13 +38,12 @@ from processview.core.superviseprocess import SuperviseProcess
 import copy
 from tomwer.core.process.reconstruction.lamino.tofu import LaminoReconstruction
 from tomwer.core.utils.Singleton import singleton
-from tomwer.web.client import OWClient
 
 logger = logging.getLogger(__name__)
 
 
 @singleton
-class LaminoReconstructionStack(qt.QObject, Queue, OWClient):
+class LaminoReconstructionStack(qt.QObject, Queue):
     """
     Manage a stack of lamino (tofu) reconstruction
     """
@@ -61,7 +60,6 @@ class LaminoReconstructionStack(qt.QObject, Queue, OWClient):
     def __init__(self, process_id=None):
         qt.QObject.__init__(self)
         Queue.__init__(self)
-        OWClient.__init__(self)
         self.process_id = process_id
         self.reconsThread = _LaminoReconsThread(process_id=process_id)
         self.reconsThread.sigThReconsFinished.connect(self._dealWithFinishedRecons)

tomwer/synctools/stacks/reconstruction/sadeltabeta.py

@@ -175,8 +175,6 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
             try:
                 sa_delta_beta.run()
             except Exception as e:
-                # TODO: for debug slurm update
-                raise e
                 _logger.error(str(e))
                 mess = "SADeltaBeta computation for {} failed.".format(str(self._scan))
                 state = DatasetState.FAILED