tomwer 1.1.1__py3-none-any.whl → 1.2.0a0__py3-none-any.whl

tomwer/app/intensitynormalization.py

@@ -1,23 +1,23 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
-import sys
 import os
-import argparse
 import signal
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
+import sys
+
 from silx.gui import qt
-from tomwer.gui import icons
-from tomwer.core.scan.scanfactory import ScanFactory
+
+from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.gui import icons
 from tomwer.gui.reconstruction.normalization.intensity import (
     SinoNormWindow as _SinoNormWindow,
 )
-from tomwer.core.process.reconstruction.normalization import (
-    SinoNormalizationTask,
-)
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 logging.basicConfig(level=logging.INFO)
 _logger = logging.getLogger(__name__)

tomwer/app/lamino.py

@@ -6,14 +6,16 @@ import logging
 import os
 import signal
 import sys
+
 from silx.gui import qt
+
 from tomwer.core.process.reconstruction.lamino.tofu import LaminoReconstruction
-from tomwer.gui.reconstruction.lamino.tofu import TofuWindow
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.gui import icons
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
+from tomwer.gui import icons
+from tomwer.gui.reconstruction.lamino.tofu import TofuWindow
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 _logger = logging.getLogger(__name__)
 # logging.getLogger().setLevel(logging.INFO)

tomwer/app/nabuapp.py

@@ -1,19 +1,21 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
+import signal
 import sys
+
 from silx.gui import qt
-import argparse
+
+from tomwer.core.process.reconstruction.nabu.nabuslices import run_slices_reconstruction
 from tomwer.core.process.reconstruction.utils.cor import relative_pos_to_absolute
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
 from tomwer.gui.reconstruction.nabu.slices import NabuDialog
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.process.reconstruction.nabu.nabuslices import run_slices_reconstruction
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 from tomwer.gui.visualization.dataviewer import DataViewer as _DataViewer
-from tomwer.core.utils.resource import increase_max_number_file
-import signal
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/nxtomoeditor.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
 import argparse
-from silx.gui import qt
+import logging
 import signal
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
+import sys
+
+from silx.gui import qt
+
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui.edit.nxtomoeditor import NXtomoEditorDialog as _NXtomoEditorDialog
-import logging
-
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/radiostack.py

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
-import sys
 import os
+import signal
+import sys
+
 from silx.gui import qt
-import argparse
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.gui.stacks import RadioStack
-from tomwer.gui import icons
+
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.utils.resource import increase_max_number_file
-import signal
+from tomwer.gui import icons
+from tomwer.gui.stacks import RadioStack
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/rsync.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import logging
-import sys
 import argparse
 import glob
+import logging
 import os
 import shutil
+import sys
+
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.synctools.utils.scanstages import ScanStages
 
-
 logging.basicConfig(level=logging.WARNING)
 logger = logging.getLogger(__name__)
 

tomwer/app/saaxis.py

@@ -1,30 +1,31 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
 import argparse
-from silx.gui import qt
-from silx.io.utils import h5py_read_dataset
+import logging
 import signal
+import sys
+import time
 from typing import Union
-from tomwer.gui import icons
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow as _SAAxisWindow
-from tomwer.core.process.reconstruction.axis.axis import AxisProcess, NoAxisUrl
-from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisProcess
-from tomwer.synctools.axis import QAxisRP
-from tomwer.synctools.saaxis import QSAAxisParams
-from tomwer.core.process.task import Task
-from tomwer.io.utils.h5pyutils import EntryReader
+
+from silx.gui import qt
+from silx.io.utils import h5py_read_dataset
+
 from tomwer.core.process import utils as core_utils
+from tomwer.core.process.reconstruction.axis.axis import AxisProcess, NoAxisUrl
 from tomwer.core.process.reconstruction.darkref.darkrefs import (
     requires_reduced_dark_and_flat,
 )
+from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisProcess
+from tomwer.core.process.task import Task
+from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.resource import increase_max_number_file
-import logging
-import time
-
+from tomwer.gui import icons
+from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow as _SAAxisWindow
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
+from tomwer.io.utils.h5pyutils import EntryReader
+from tomwer.synctools.axis import QAxisRP
+from tomwer.synctools.saaxis import QSAAxisParams
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)
@@ -46,7 +47,7 @@ class SAAxisThread(qt.QThread):
         process.dump_roi = self._dump_roi
         t0 = time.time()
         process.run()
-        print("execution time is {}".format(time.time() - t0))
+        print(f"execution time is {time.time() - t0}")
 
 
 class SAAxisWindow(_SAAxisWindow):
@@ -96,12 +97,10 @@ class SAAxisWindow(_SAAxisWindow):
         qt.QApplication.restoreOverrideCursor()
 
     def _callbackStartLoadSinogram(self):
-        print(
-            "start loading sinogram for {}. Can take some time".format(self.getScan())
-        )
+        print(f"start loading sinogram for {self.getScan()}. Can take some time")
 
     def _callbackEndLoadSinogram(self):
-        print("sinogram loaded for {} loaded.".format(self.getScan()))
+        print(f"sinogram loaded for {self.getScan()} loaded.")
 
     def close(self) -> None:
         self._stopProcessingThread()
@@ -128,7 +127,7 @@ class SAAxisWindow(_SAAxisWindow):
             }
         )
 
-        _logger.info("{} - start cor estimation for".format(scan))
+        _logger.info(f"{scan} - start cor estimation for")
         qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
         try:
             _cor_estimation_process.compute(scan=scan, wait=True)
@@ -270,7 +269,7 @@ def _load_latest_scores(scan) -> tuple:
                     latest_saaxis_node["results"]["center_of_rotation"]
                 )
         else:
-            _logger.warning("no results found for {}".format(scan))
+            _logger.warning(f"no results found for {scan}")
     return scores, selected
 
 

tomwer/app/sadeltabeta.py

@@ -1,36 +1,36 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
 import argparse
-from silx.gui import qt
+import logging
 import signal
+import sys
+import time
 from typing import Union
-from tomwer.gui import icons
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.core.scan.scanfactory import ScanFactory
+
+from silx.gui import qt
 from silx.io.utils import h5py_read_dataset
+
+from tomwer.core.process import utils as core_utils
+from tomwer.core.process.reconstruction.axis.axis import AxisProcess, NoAxisUrl
+from tomwer.core.process.reconstruction.darkref.darkrefs import (
+    requires_reduced_dark_and_flat,
+)
 from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
     SADeltaBetaProcess,
 )
+from tomwer.core.process.task import Task
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.utils.resource import increase_max_number_file
+from tomwer.gui import icons
+from tomwer.gui.reconstruction.saaxis.saaxis import NabuAutoCorDiag
 from tomwer.gui.reconstruction.sadeltabeta.saadeltabeta import (
     SADeltaBetaWindow as _SADeltaBetaWindow,
 )
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
+from tomwer.io.utils.h5pyutils import EntryReader
 from tomwer.synctools.axis import QAxisRP
-from tomwer.gui.reconstruction.saaxis.saaxis import NabuAutoCorDiag
-from tomwer.core.process.reconstruction.axis.axis import AxisProcess
-from tomwer.core.process.reconstruction.axis.axis import NoAxisUrl
 from tomwer.synctools.sadeltabeta import QSADeltaBetaParams
-from tomwer.core.process.task import Task
-from tomwer.io.utils.h5pyutils import EntryReader
-from tomwer.core.process import utils as core_utils
-from tomwer.core.process.reconstruction.darkref.darkrefs import (
-    requires_reduced_dark_and_flat,
-)
-from tomwer.core.utils.resource import increase_max_number_file
-import logging
-import time
-
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)
@@ -52,7 +52,7 @@ class SADeltaBetaThread(qt.QThread):
         process.dump_roi = self._dump_roi
         t0 = time.time()
         process.run()
-        print("execution time is {}".format(time.time() - t0))
+        print(f"execution time is {time.time() - t0}")
 
 
 class SADeltaBetaWindow(_SADeltaBetaWindow):
@@ -202,7 +202,7 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
             inputs={"data": scan, "axis_params": self._qaxis_rp}
         )
 
-        _logger.info("{} - start cor estimation for".format(scan))
+        _logger.info(f"{scan} - start cor estimation for")
         qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
         try:
             _cor_estimation_process.compute(scan=scan, wait=True)
@@ -340,7 +340,7 @@ def _load_latest_scores(scan) -> tuple:
             if "delta_beta" in latest_sa_db_node["results"]:
                 selected = h5py_read_dataset(latest_sa_db_node["results"]["delta_beta"])
         else:
-            _logger.warning("no results found for {}".format(scan))
+            _logger.warning(f"no results found for {scan}")
     return scores, selected
 
 

tomwer/app/samplemoved.py

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
+import os
+import signal
 import sys
+
 from silx.gui import qt
-import argparse
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.gui import icons
+
 from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.gui.samplemoved import SampleMovedWidget
 from tomwer.core.utils.resource import increase_max_number_file
-import os
-import signal
+from tomwer.gui import icons
+from tomwer.gui.samplemoved import SampleMovedWidget
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/scanviewer.py

@@ -1,17 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
 import argparse
-from silx.gui import qt
+import logging
 import signal
+import sys
+
+from silx.gui import qt
+
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui.visualization.dataviewer import DataViewer
-from tomwer.core.utils.resource import increase_max_number_file
-import logging
-
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/sinogramviewer.py

@@ -1,17 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
+import signal
 import sys
+import weakref
+
 from silx.gui import qt
-import argparse
+
+from tomwer.core.scan.scanfactory import ScanFactory
+from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui.visualization.sinogramviewer import SinogramViewer as _SinogramViewer
-from tomwer.core.utils.resource import increase_max_number_file
-import signal
-import weakref
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)
@@ -91,8 +93,7 @@ def main(argv):
         raise ValueError("Line value should be at least 0")
     if options.line > scan.dim_2:
         raise ValueError(
-            "Line value is outside frame dimension."
-            "Should be at most {}".format(scan.dim_2)
+            f"Line value is outside frame dimension. Should be at most {scan.dim_2}"
         )
 
     widget = SinogramViewer(parent=None)

tomwer/app/slicestack.py

@@ -1,16 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import logging
-import sys
 import os
+import signal
+import sys
+
 from silx.gui import qt
-import argparse
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.gui.stacks import SliceStack
-from tomwer.gui import icons
+
 from tomwer.core.utils.resource import increase_max_number_file
-import signal
+from tomwer.gui import icons
+from tomwer.gui.stacks import SliceStack
+from tomwer.gui.utils.splashscreen import getMainSplashScreen
 
 logging.basicConfig(level=logging.WARNING)
 _logger = logging.getLogger(__name__)

tomwer/app/stopdatalistener.py

@@ -3,11 +3,12 @@
 
 import argparse
 import sys
+from signal import SIGKILL, SIGTERM
+
 from tomwer.core.process.control.datalistener.rpcserver import (
     send_signal_to_local_rpc_servers,
 )
 from tomwer.core.settings import JSON_RPC_PORT
-from signal import SIGTERM, SIGKILL
 
 
 def getinputinfo():

tomwer/core/futureobject.py

@@ -28,16 +28,15 @@ __license__ = "MIT"
 __date__ = "09/10/2021"
 
 
-import logging
-from tomwer.core.scan.scanbase import TomwerScanBase
-from typing import Optional
-from typing import Iterable
-from typing import Union
 import datetime
+import logging
+from typing import Iterable, Optional, Union
 
-from tomwer.core.tomwer_object import TomwerObject
 from sluurp.job import get_job_status
 
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.tomwer_object import TomwerObject
+
 _logger = logging.getLogger(__name__)
 
 
@@ -110,6 +109,16 @@ class FutureTomwerObject:
                 return status
         return "finished"
 
+    @property
+    def logs(self) -> str:
+        new_line = "\n"
+        return "\n".join(
+            [
+                f"~~~~~~ job id = {fut.job_id} ~~~~~{new_line}{f'{new_line}'.join(fut.collect_logs() or ['',])}"
+                for fut in self._futures
+            ]
+        )
+
     @property
     def start_time(self) -> Optional[datetime.time]:
         return self._start_time

tomwer/core/log/logger.py

@@ -34,16 +34,17 @@ __license__ = "MIT"
 __date__ = "22/09/2017"
 
 import logging
+import os
 from sys import platform
+
 from tomwer.core.log.processlog import (
     PROCESS_ENDED_NAME,
-    PROCESS_SKIPPED_NAME,
+    PROCESS_FAILED_NAME,
     PROCESS_INFORM_NAME,
+    PROCESS_SKIPPED_NAME,
     PROCESS_STARTED_NAME,
-    PROCESS_FAILED_NAME,
     PROCESS_SUCCEED_NAME,
 )
-import os
 
 # The background is set with 40 plus the number of the color, and the
 # foreground with 30

tomwer/core/log/processlog.py

@@ -33,7 +33,6 @@ __date__ = "02/10/2020"
 
 import logging
 
-
 PROCESS_STARTED_NAME = "PROCESS_STARTED"
 PROCESS_STARTED_LEVEL = 32
 

tomwer/core/process/conditions/filters.py

@@ -33,13 +33,13 @@ __date__ = "19/07/2018"
 
 import fnmatch
 import logging
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.scan.scanfactory import ScanFactory
-import tomwer.version
 import os
 import re
 
+import tomwer.version
 from tomwer.core.process.task import Task
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.core.scan.scanfactory import ScanFactory
 
 _logger = logging.getLogger(__name__)
 

tomwer/core/process/control/datadiscovery.py

@@ -0,0 +1,7 @@
+from ewokscore.task import Task as EwoksTask
+from tomwer.core.utils.scanutils import data_identifier_to_scan
+
+
+class _DataDiscoveryPlaceHolder(EwoksTask, input_names=["data"], output_names=["data"]):
+    def run(self):
+        self.outputs.data = data_identifier_to_scan(self.inputs.data)

tomwer/core/process/control/datalistener/datalistener.py

@@ -28,21 +28,24 @@ __license__ = "MIT"
 __date__ = "05/07/2017"
 
 
-import socket
-import os
-from tomwer.core import settings
-import tomwer.version
-from tomwer.core.process.task import BaseProcessInfo
 import logging
-from .rpcserver import DataListenerThread
+import os
+import socket
+import time
+import typing
+
+from ewokscore.task import Task as EwoksTask
 from nxtomomill import converter as nxtomomill_converter
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomoscan.io import HDF5File
 from silx.io.utils import h5py_read_dataset
-from ewokscore.task import Task as EwoksTask
+from tomoscan.io import HDF5File
+
+import tomwer.version
+from tomwer.core import settings
+from tomwer.core.process.task import BaseProcessInfo
 from tomwer.core.scan.blissscan import BlissScan
-import typing
-import time
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+
+from .rpcserver import DataListenerThread
 
 try:
     # new HDF5Config class
@@ -66,10 +69,11 @@ def nxtomomill_input_callback(entry, desc):
     """note: for the data listener we want to avoid any user intereaction.
     In order to avoid any time lost"""
     if entry == "energy":
-        _logger.warning("Energy is missing {}. set to {}".format(entry, 19.0))
-        return 19.0
+        default_energy = 19.0
+        _logger.warning(f"Energy is missing. Set it to default to {default_energy}")
+        return default_energy
     else:
-        _logger.warning("missing {}. Won't be set".format(entry))
+        _logger.warning(f"missing {entry}. Won't be set")
         return None
 
 
@@ -163,7 +167,7 @@ class DataListener(BaseProcessInfo):
         elif isinstance(properties, dict):
             self._settings = properties
         else:
-            raise TypeError("invalid type: {}".format(type(properties)))
+            raise TypeError(f"invalid type: {type(properties)}")
 
     def run(self):
         pass
@@ -182,7 +186,7 @@ class DataListener(BaseProcessInfo):
         :return: tuple scan succeeded.
         """
         if not os.path.isfile(sample_file):
-            raise ValueError("Given file {} does not exists.".format(sample_file))
+            raise ValueError(f"Given file {sample_file} does not exists.")
         scans = []
         for mf_emf in self.convert(bliss_file=sample_file, entry=entry):
             master_file, entry_master_file = mf_emf
@@ -507,9 +511,7 @@ class DataListener(BaseProcessInfo):
             time.sleep(0.2)
 
         if timeout <= 0:
-            _logger.error(
-                "unable to access {}@{}. (Write never ended)".format(entry, bliss_file)
-            )
+            _logger.error(f"unable to access {entry}@{bliss_file}. (Write never ended)")
             return ((None, None),)
         # one more delay to insure we can read it. Some frame might need more time to be dump from lima.
         time.sleep(4)
@@ -530,8 +532,7 @@ class DataListener(BaseProcessInfo):
             )
         except Exception as e:
             _logger.error(
-                "Fail to convert from tango file: %s to NXTomo."
-                "Conversion error is: %s" % (bliss_file, e)
+                f"Fail to convert from tango file: {bliss_file} to NXTomo. Error is: {e}"
             )
             return ((None, None),)
         else: