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

tomwer/core/scan/test/test_scan.py

@@ -27,21 +27,23 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "24/01/2017"
 
-import unittest
+import contextlib
 import logging
+import os
+import shutil
 import tempfile
-import numpy
+import unittest
+from multiprocessing import Process
+
 import fabio.edfimage
-import contextlib
+import numpy
+
+from tomwer.core.process.reconstruction.nabu import nabuslices
+from tomwer.core.process.task import Task
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.process.task import Task
-from tomwer.tests.utils import UtilsTest
 from tomwer.core.utils.scanutils import MockEDF
-from tomwer.core.process.reconstruction.nabu import nabuslices
-import shutil
-import os
-from multiprocessing import Process
+from tomwer.tests.utils import UtilsTest
 
 logging.disable(logging.INFO)
 

tomwer/core/settings.py

@@ -30,7 +30,6 @@ __date__ = "02/06/2017"
 
 import os
 
-
 __LBSRAM_PATH = '/lbsram'
 
 __DEST_PATH = ''
@@ -104,7 +103,7 @@ class SlurmSettings:
     N_GPUS_PER_WORKER = 1
     """number of gpu per worker"""
 
-    PYTHON_VENV = "/scisoft/tomotools/activate.sh stable"
+    PYTHON_VENV = "/scisoft/tomotools/activate stable"
     """Python executable to take. Useful if compute nodes have a different environment from the front end.
     """
 

tomwer/core/test/test_lamino.py

@@ -27,9 +27,10 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "19/07/2018"
 
-import unittest
-import tempfile
 import shutil
+import tempfile
+import unittest
+
 from tomwer.core.process.reconstruction.lamino import tofu
 from tomwer.core.scan.edfscan import EDFTomoScan
 

tomwer/core/test/test_scanutils.py

@@ -27,11 +27,12 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "30/09/2019"
 
-import unittest
 import os
 import tempfile
-from tomwer.core.utils.scanutils import MockHDF5
+import unittest
+
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.utils.scanutils import MockHDF5
 
 
 class TestMockHDF5(unittest.TestCase):

tomwer/core/test/test_utils.py

@@ -28,15 +28,17 @@ __license__ = "MIT"
 __date__ = "02/08/2017"
 
 
-import unittest
-import tempfile
 import os
 import shutil
+import tempfile
+import unittest
+
+import numpy
+
 from tomwer.core import utils
+from tomwer.core.utils.normalization import flatFieldCorrection
 from tomwer.core.utils.scanutils import MockEDF, MockHDF5
 from tomwer.tests.utils import UtilsTest
-from tomwer.core.utils.normalization import flatFieldCorrection
-import numpy
 
 
 class TestGetClosestEnergy(unittest.TestCase):

tomwer/core/utils/__init__.py

@@ -27,16 +27,18 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "17/05/2017"
 
-import fabio.edfimage
-import os
-import psutil
+import fileinput
 import logging
+import os
 import shutil
-from tomwer.core import settings
-from tomoscan.unitsystem import metricsystem
 from urllib.request import urlopen
-import fileinput
+
+import fabio.edfimage
+import psutil
 from lxml import etree
+from tomoscan.unitsystem import metricsystem
+
+from tomwer.core import settings
 
 logger = logging.getLogger(__name__)
 

tomwer/core/utils/deprecation.py

@@ -28,9 +28,9 @@ __authors__ = ["Jerome Kieffer", "H. Payno", "P. Knobel"]
 __license__ = "MIT"
 __date__ = "26/02/2018"
 
-import sys
-import logging
 import functools
+import logging
+import sys
 import traceback
 
 depreclog = logging.getLogger("silx.DEPRECATION")

tomwer/core/utils/image.py

@@ -28,9 +28,10 @@ __license__ = "MIT"
 __date__ = "25/02/2019"
 
 
-import numpy
-import logging
 import enum
+import logging
+
+import numpy
 from numpy.linalg import inv
 
 _logger = logging.getLogger(__file__)
@@ -67,7 +68,7 @@ def shift_img(
     assert data.ndim == 2
     assert dx is not None
     assert dy is not None
-    _logger.debug("apply shift dx=%s, dy=%s " % (dx, dy))
+    _logger.debug(f"apply shift dx={dx}, dy={dy} ")
 
     if use_scipy and has_scipy_shift:
         return shift_scipy(

tomwer/core/utils/locker.py

@@ -30,8 +30,8 @@ __date__ = "20/04/2020"
 
 import os
 import threading
-
 from contextlib import AbstractContextManager
+
 from tomwer.core.utils.Singleton import singleton
 
 

tomwer/core/utils/normalization.py

@@ -29,6 +29,7 @@ __date__ = "30/05/2018"
 
 
 import logging
+
 import fabio
 
 _logger = logging.getLogger(__name__)

tomwer/core/utils/nxtomoutils.py

@@ -29,8 +29,9 @@ __date__ = "02/12/2021"
 
 
 from typing import Union
-from tomoscan.esrf.scan.hdf5scan import ImageKey
+
 import numpy
+from tomoscan.esrf.scan.hdf5scan import ImageKey
 
 
 def get_n_series(image_key_values: Union[tuple, list], image_key_type: ImageKey) -> int:

tomwer/core/utils/scanutils.py

@@ -30,18 +30,21 @@ __license__ = "MIT"
 __date__ = "11/08/2022"
 
 import logging
-import h5py
-import numpy
-import time
 import os
+import time
 from typing import Any
+
+import h5py
+import numpy
+from silx.io.utils import h5py_read_dataset
+from tomoscan.esrf.scan.mock import MockEDF as _MockEDF
+from tomoscan.esrf.scan.mock import MockHDF5 as _MockHDF5
 from tomoscan.io import HDF5File
-from tomoscan.esrf.scan.mock import MockEDF as _MockEDF, MockHDF5 as _MockHDF5
 from tomoscan.test.utils import MockContext
+
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.scan.scanfactory import ScanFactory
-from silx.io.utils import h5py_read_dataset
 
 _logger = logging.getLogger(__name__)
 
@@ -273,7 +276,7 @@ class _BlissSample:
             h5f["/".join((str(seq_ini_index) + ".1", "end_time"))] = str(time.ctime())
 
         if self.__with_nx:
-            nx_file = "sample_{}.nx".format(str(seq_ini_index).zfill(4))
+            nx_file = f"sample_{seq_ini_index:04}.nx"
             nx_file = os.path.join(self.path, nx_file)
             with h5py.File(nx_file, "a") as h5f:
                 pass

tomwer/core/utils/slurm.py

@@ -30,8 +30,9 @@ __license__ = "MIT"
 __date__ = "11/10/2021"
 
 
-from datetime import datetime
 import uuid
+from datetime import datetime
+
 from sluurp.utils import has_sbatch_available
 
 

tomwer/core/utils/time.py

@@ -44,7 +44,5 @@ class Timer:
         self._start_time = time()
 
     def __exit__(self, type, value, traceback):
-        print(
-            "{title} exec time: {exec_time} s"
-            "".format(title=self.title, exec_time=(time() - self._start_time))
-        )
+        exec_time = time() - self._start_time
+        print(f"{self.title} exec time: {exec_time} s")

tomwer/core/utils/volumeutils.py

@@ -1,6 +1,7 @@
-from tomwer.core.volume.volumefactory import VolumeFactory
 from typing import Any
 
+from tomwer.core.volume.volumefactory import VolumeFactory
+
 
 def volume_identifier_to_volume(volume_identifier: Any):
     """

tomwer/core/volume/__init__.py

@@ -1,5 +1,5 @@
 from .edfvolume import EDFVolume  # noqa F401
 from .hdf5volume import HDF5Volume  # noqa F401
 from .jp2kvolume import JP2KVolume  # noqa F401
-from .tiffvolume import TIFFVolume, MultiTIFFVolume  # noqa F401
 from .rawvolume import RawVolume  # noqa F401
+from .tiffvolume import MultiTIFFVolume, TIFFVolume  # noqa F401

tomwer/core/volume/edfvolume.py

@@ -28,12 +28,13 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.edfvolume import EDFVolume as _EDFVolume
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.edfidentifier import (
     EDFVolumeIdentifier as _EDFVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
+from tomoscan.esrf.volume.edfvolume import EDFVolume as _EDFVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class EDFVolumeIdentifier(_EDFVolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/hdf5volume.py

@@ -28,18 +28,16 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.hdf5volume import HDF5Volume as _HDF5Volume
+from urllib.parse import urlparse
+
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.hdf5Identifier import (
     HDF5VolumeIdentifier as _HDF5VolumeIdentifier,
 )
+from tomoscan.esrf.identifier.url_utils import UrlSettings, split_path, split_query
+from tomoscan.esrf.volume.hdf5volume import HDF5Volume as _HDF5Volume
+
 from tomwer.core.volume.volumebase import TomwerVolumeBase
-from processview.core.dataset import DatasetIdentifier, Dataset
-from urllib.parse import urlparse
-from tomoscan.esrf.identifier.url_utils import (
-    UrlSettings,
-    split_path,
-    split_query,
-)
 
 
 class HDF5VolumeIdentifier(_HDF5VolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/jp2kvolume.py

@@ -28,12 +28,13 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.jp2kvolume import JP2KVolume as _JP2KVolume
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.jp2kidentifier import (
     JP2KVolumeIdentifier as _JP2KVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
+from tomoscan.esrf.volume.jp2kvolume import JP2KVolume as _JP2KVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class JP2KVolumeIdentifier(_JP2KVolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/rawvolume.py

@@ -28,16 +28,16 @@ __license__ = "MIT"
 __date__ = "11/01/2023"
 
 
-from tomoscan.esrf.volume.rawvolume import RawVolume as _RawVolume
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+from urllib.parse import urlparse
+
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.rawidentifier import (
     RawVolumeIdentifier as _RawVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
-from urllib.parse import urlparse
-from tomoscan.esrf.identifier.url_utils import (
-    split_path,
-)
+from tomoscan.esrf.identifier.url_utils import split_path
+from tomoscan.esrf.volume.rawvolume import RawVolume as _RawVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class RawVolumeIdentifier(_RawVolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/tiffvolume.py

@@ -29,16 +29,18 @@ __date__ = "05/07/2022"
 
 
 import os
-from tomoscan.esrf.volume.tiffvolume import (
-    TIFFVolume as _TIFFVolume,
-    MultiTIFFVolume as _MultiTIFFVolume,
-)
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.tiffidentifier import (
     MultiTiffVolumeIdentifier as _MultiTiffVolumeIdentifier,
+)
+from tomoscan.esrf.identifier.tiffidentifier import (
     TIFFVolumeIdentifier as _TIFFVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
+from tomoscan.esrf.volume.tiffvolume import MultiTIFFVolume as _MultiTIFFVolume
+from tomoscan.esrf.volume.tiffvolume import TIFFVolume as _TIFFVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class TIFFVolumeIdentifier(_TIFFVolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/volumebase.py

@@ -1,4 +1,5 @@
 import os
+
 from tomwer.core.tomwer_object import TomwerObject
 
 

tomwer/core/volume/volumefactory.py

@@ -28,34 +28,34 @@ __license__ = "MIT"
 __date__ = "13/07/2022"
 
 
-from typing import Optional
+import logging
+from typing import Optional, Union
 from urllib.parse import urlparse
-from typing import Union
-from tomoscan.factory import Factory as _oVolumeFactory
+
+from tomoscan import identifier as _identifier_mod
 from tomoscan.esrf.identifier.url_utils import split_path
+from tomoscan.factory import Factory as _oVolumeFactory
 from tomoscan.identifier import BaseIdentifier, ScanIdentifier, VolumeIdentifier
-from tomoscan import identifier as _identifier_mod
+
+from tomwer.core.scan.edfscan import EDFTomoScan, EDFTomoScanIdentifier
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.volume import (
+    EDFVolume,
+    HDF5Volume,
+    JP2KVolume,
+    MultiTIFFVolume,
+    RawVolume,
+    TIFFVolume,
+)
 from tomwer.core.volume.edfvolume import EDFVolumeIdentifier
-from tomwer.core.scan.edfscan import EDFTomoScanIdentifier
 from tomwer.core.volume.hdf5volume import HDF5VolumeIdentifier
 from tomwer.core.volume.jp2kvolume import JP2KVolumeIdentifier
+from tomwer.core.volume.rawvolume import RawVolumeIdentifier
 from tomwer.core.volume.tiffvolume import (
-    TIFFVolumeIdentifier,
     MultiTiffVolumeIdentifier,
+    TIFFVolumeIdentifier,
 )
-from tomwer.core.volume.rawvolume import RawVolumeIdentifier
-from tomwer.core.volume import (
-    HDF5Volume,
-    EDFVolume,
-    MultiTIFFVolume,
-    TIFFVolume,
-    JP2KVolume,
-    RawVolume,
-)
-from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.utils import docstring
-import logging
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/cluster/slurm.py

@@ -29,7 +29,9 @@ __date__ = "11/10/2021"
 
 
 from typing import Optional
+
 from silx.gui import qt
+
 from tomwer.core.settings import SlurmSettings
 
 

tomwer/gui/cluster/supervisor.py

@@ -28,10 +28,12 @@ __license__ = "MIT"
 __date__ = "14/10/2021"
 
 
+import functools
+from collections import OrderedDict
+
 from silx.gui import qt
+
 from tomwer.core.futureobject import FutureTomwerObject
-from collections import OrderedDict
-import functools
 
 
 class FutureTomwerScanObserverWidget(qt.QWidget):

tomwer/gui/cluster/test/test_cluster.py

@@ -27,12 +27,13 @@ __license__ = "MIT"
 __date__ = "19/10/2021"
 
 
-from tomwer.gui.reconstruction.nabu.slurm import SlurmSettingsWidget
-from tomwer.core.settings import SlurmSettings
-from silx.gui.utils.testutils import TestCaseQt
+import pytest
 from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from tomwer.core.settings import SlurmSettings
+from tomwer.gui.reconstruction.nabu.slurm import SlurmSettingsWidget
 from tomwer.tests.utils import skip_gui_test
-import pytest
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")

tomwer/gui/cluster/test/test_supervisor.py

@@ -30,11 +30,13 @@ __date__ = "08/11/2021"
 import asyncio
 import os
 import shutil
+import tempfile
+
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
-import tempfile
-from tomwer.core.utils.scanutils import MockHDF5
+
 from tomwer.core.futureobject import FutureTomwerObject
+from tomwer.core.utils.scanutils import MockHDF5
 from tomwer.gui.cluster.supervisor import FutureTomwerScanObserverWidget
 
 

tomwer/gui/conditions/filter.py

@@ -33,12 +33,13 @@ __date__ = "19/07/2018"
 
 
 from silx.gui import qt
+
+from tomwer.core.process.conditions.filters import FileNameFilter
 from tomwer.gui import icons
 from tomwer.gui.utils.sandboxes import (
     RegularExpressionSandBox,
     RegularExpressionSandBoxDialog,
 )
-from tomwer.core.process.conditions.filters import FileNameFilter
 
 
 class FileNameFilterWidget(qt.QWidget):
@@ -126,14 +127,14 @@ class FileNameFilterWidget(qt.QWidget):
         mess.setModal(False)
         mess.show()
 
-    def setActiveFilter(self, filter):
+    def setActiveFilter(self, filter_):
         valid_fiters = ("regular expression", "unix file name pattern")
-        if filter not in valid_fiters:
+        if filter_ not in valid_fiters:
             raise ValueError(
-                f"filter is expected to be one of {valid_fiters}. Not {filter}"
+                f"filter is expected to be one of {valid_fiters}. Not {filter_}"
             )
-        self._sandBoxPB.setVisible(filter == "regular expression")
-        self._filterTypeCB.setCurrentText(filter)
+        self._sandBoxPB.setVisible(filter_ == "regular expression")
+        self._filterTypeCB.setCurrentText(filter_)
 
     def getActiveFilter(self):
         return self._filterTypeCB.currentText()

tomwer/gui/control/actions.py

@@ -29,6 +29,7 @@ __date__ = "23/03/2021"
 
 
 from silx.gui import qt
+
 from tomwer.gui import icons as tomwer_icons