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

tomwer/gui/reconstruction/lamino/tofu/projections.py

@@ -28,19 +28,27 @@ __license__ = "MIT"
 __date__ = "01/06/2018"
 
 
+import logging
 import os
+
 from silx.gui import qt
-import logging
-from tomwer.core.process.reconstruction.lamino.tofu import getDark, getFlats, FFCWhen
-from tomwer.core.utils import getDARK_N, getDim1Dim2
-from tomwer.core.utils import getParametersFromParOrInfo
-from tomwer.core.utils import getTomo_N, getPixelSize, getClosestEnergy
+
+from tomwer.core.process.reconstruction.lamino.tofu import FFCWhen, getDark, getFlats
+from tomwer.core.utils import (
+    getClosestEnergy,
+    getDARK_N,
+    getDim1Dim2,
+    getParametersFromParOrInfo,
+    getPixelSize,
+    getTomo_N,
+)
 from tomwer.core.utils.char import PSI_CHAR, THETA_CHAR
 from tomwer.gui import icons
-from tomwer.gui.utils.illustrations import _IllustrationWidget, _IllustrationDialog
+from tomwer.gui.utils.illustrations import _IllustrationDialog, _IllustrationWidget
 from tomwer.gui.utils.unitsystem import MetricEntry
-from .TofuOptionLoader import _TofuOptionLoader, _getterSetter
-from .misc import _AngleWidget, PadlockButton
+
+from .misc import PadlockButton, _AngleWidget
+from .TofuOptionLoader import _getterSetter, _TofuOptionLoader
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/lamino/tofu/tofu.py

@@ -30,21 +30,24 @@ __license__ = "MIT"
 __date__ = "01/06/2018"
 
 
+import logging
+
 from silx.gui import qt
 from silx.io import dictdump
-import logging
+
 from tomwer.core.process.reconstruction.lamino.tofu import (
     SCAN_TYPES,
     SCAN_TYPES_I,
     FFCWhen,
+    _retrieve_opts_recons_cmd,
 )
-from tomwer.core.process.reconstruction.lamino.tofu import _retrieve_opts_recons_cmd
 from tomwer.core.utils.char import PSI_CHAR
 from tomwer.gui import icons
 from tomwer.gui.reconstruction.lamino.tofu import settings
-from .TofuOptionLoader import _TofuOptionLoader, _getterSetter
+
 from .projections import InputProjectionsScrollArea
 from .tofuexpert import ExpertTofuWidget
+from .TofuOptionLoader import _getterSetter, _TofuOptionLoader
 from .tofuoutput import OutputTofuWidget
 
 _logger = logging.getLogger(__name__)

tomwer/gui/reconstruction/lamino/tofu/tofuexpert.py

@@ -28,12 +28,15 @@ __license__ = "MIT"
 __date__ = "01/06/2018"
 
 
+import logging
 import subprocess
+
 from silx.gui import qt
+
 import tomwer.core.utils.gpu
 from tomwer.core.process.reconstruction.lamino.tofu import has_tofu
-import logging
-from .TofuOptionLoader import _TofuOptionLoader, _getterSetter
+
+from .TofuOptionLoader import _getterSetter, _TofuOptionLoader
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/lamino/tofu/tofuoutput.py

@@ -28,21 +28,24 @@ __license__ = "MIT"
 __date__ = "01/06/2018"
 
 
+import logging
 import os
+
 from silx.gui import qt
-import logging
+
 from tomwer.core.process.reconstruction.lamino.tofu import (
-    SLICE_STACK_TYPE,
-    ROTATION_CENTER_TYPE,
     LAMINO_ANGLE_TYPE,
     PSI_ANGLE_TYPE,
+    ROTATION_CENTER_TYPE,
+    SLICE_STACK_TYPE,
 )
 from tomwer.core.settings import get_lbsram_path
 from tomwer.core.utils.char import DELTA_CHAR
 from tomwer.gui.reconstruction.lamino.tofu import settings
 from tomwer.gui.utils.illustrations import _IllustrationWidget
-from .TofuOptionLoader import _TofuOptionLoader, _getterSetter
-from .misc import _AngleWidget, _RegionLE, PadlockButton
+
+from .misc import PadlockButton, _AngleWidget, _RegionLE
+from .TofuOptionLoader import _getterSetter, _TofuOptionLoader
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/nabu/action.py

@@ -29,6 +29,7 @@ __date__ = "04/08/2020"
 
 
 from silx.gui import qt
+
 from tomwer.gui import icons as tomwer_icons
 
 

tomwer/gui/reconstruction/nabu/castvolume.py

@@ -28,18 +28,20 @@ __license__ = "MIT"
 __date__ = "15/12/2021"
 
 
+import logging
+from typing import Optional
+
 from silx.gui import qt
+from silx.gui.utils import blockSignals
+
 from tomwer.core.process.reconstruction.nabu.castvolume import (
+    DEFAULT_OUTPUT_DIR,
     RESCALE_MAX_PERCENTILE,
     RESCALE_MIN_PERCENTILE,
-    DEFAULT_OUTPUT_DIR,
 )
 from tomwer.core.process.reconstruction.nabu.nabucommon import NabuOutputFileFormat
 from tomwer.gui.qlefilesystem import QLFileSystem
 from tomwer.gui.reconstruction.nabu.nabuconfig.output import QNabuFileFormatComboBox
-from silx.gui.utils import blockSignals
-import logging
-from typing import Optional
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/nabu/check.py

@@ -28,10 +28,11 @@ __license__ = "MIT"
 __date__ = "02/12/2021"
 
 
+from silx.gui import qt
+from tomoscan.esrf.scan.hdf5scan import ImageKey
+
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.utils.nxtomoutils import get_n_series
-from tomoscan.esrf.scan.hdf5scan import ImageKey
-from silx.gui import qt
 
 
 def check_dark_series(scan: HDF5TomoScan, logger=None, user_input: bool = True) -> bool:

tomwer/gui/reconstruction/nabu/nabuconfig/base.py

@@ -29,8 +29,11 @@ __date__ = "11/02/2020"
 
 
 from typing import Union
-from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
-from tomwer.core.process.reconstruction.nabu.utils import ConfigurationLevel
+
+from tomwer.core.process.reconstruction.nabu.utils import (
+    ConfigurationLevel,
+    _NabuStages,
+)
 
 
 class _FilteringObject:

tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py

@@ -1,10 +1,13 @@
-from silx.gui import qt
 from typing import Optional, Union
+
+from silx.gui import qt
+from silx.gui.utils import blockSignals
+from silx.utils.enum import Enum as _Enum
+
 from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 from tomwer.gui.reconstruction.nabu.nabuconfig import base
 from tomwer.gui.utils.illustrations import _IllustrationWidget
-from silx.gui.utils import blockSignals
-from silx.utils.enum import Enum as _Enum
+
 from .reconstruction import AnglesFileWidget as Filewidget
 
 

tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py

@@ -29,15 +29,16 @@ __date__ = "11/02/2020"
 
 
 from silx.gui import qt
+
+from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
+from tomwer.gui.reconstruction.nabu.nabuconfig.output import _NabuOutputConfig
+from tomwer.gui.reconstruction.nabu.nabuconfig.phase import _NabuPhaseConfig
 from tomwer.gui.reconstruction.nabu.nabuconfig.preprocessing import (
     _NabuPreProcessingConfig,
 )
-from tomwer.gui.reconstruction.nabu.nabuconfig.phase import _NabuPhaseConfig
 from tomwer.gui.reconstruction.nabu.nabuconfig.reconstruction import (
     _NabuReconstructionConfig,
 )
-from tomwer.gui.reconstruction.nabu.nabuconfig.output import _NabuOutputConfig
-from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 
 
 class NabuConfiguration(qt.QWidget):

tomwer/gui/reconstruction/nabu/nabuconfig/output.py

@@ -28,14 +28,16 @@ __license__ = "MIT"
 __date__ = "11/02/2020"
 
 
+import logging
 import os
 import typing
+
 from silx.gui import qt
+
 from tomwer.core.process.reconstruction.nabu.nabucommon import NabuOutputFileFormat
+from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 from tomwer.gui.qlefilesystem import QLFileSystem
 from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
-from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
-import logging
 from tomwer.io.utils import get_default_directory
 
 try:
@@ -145,12 +147,12 @@ class NabuOutputLocationWidget(qt.QWidget):
         else:
             return self._outputDirQLE.text()
 
-    def setOutputDir(self, dir):
-        if dir in (None, ""):
+    def setOutputDir(self, output_dir):
+        if output_dir in (None, ""):
             self._defaultOutput.setChecked(True)
         else:
             self._defaultOutput.setChecked(False)
-            self._outputDirQLE.setText(dir)
+            self._outputDirQLE.setText(output_dir)
 
 
 class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):

tomwer/gui/reconstruction/nabu/nabuconfig/phase.py

@@ -28,17 +28,19 @@ __license__ = "MIT"
 __date__ = "11/02/2020"
 
 
+import logging
 import typing
-from tomwer.utils import docstring
+
 from silx.gui import qt
-from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
+from silx.utils.enum import Enum as _Enum
+
+from tomwer.core.process.reconstruction.nabu.utils import _NabuPhaseMethod, _NabuStages
+from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 from tomwer.gui.reconstruction.nabu.nabuconfig import base
 from tomwer.gui.reconstruction.nabu.nabuconfig.ctf import CTFConfig
 from tomwer.gui.utils.inputwidget import SelectionLineEdit
-from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
-from tomwer.core.process.reconstruction.nabu.utils import _NabuStages, _NabuPhaseMethod
-import logging
-from silx.utils.enum import Enum as _Enum
+from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
+from tomwer.utils import docstring
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -28,19 +28,19 @@ __license__ = "MIT"
 __date__ = "06/12/2021"
 
 
+import logging
 from typing import Optional
+
 from silx.gui import qt
-from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
-from tomwer.utils import docstring
+
 from tomwer.core.process.reconstruction.nabu.utils import (
     _NabuStages,
     _RingCorrectionMethod,
 )
-from tomwer.gui.utils.scrollarea import (
-    QComboBoxIgnoreWheel as QComboBox,
-    QDoubleSpinBoxIgnoreWheel as QDoubleSpinBox,
-)
-import logging
+from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
+from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
+from tomwer.gui.utils.scrollarea import QDoubleSpinBoxIgnoreWheel as QDoubleSpinBox
+from tomwer.utils import docstring
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py

@@ -27,26 +27,29 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "12/02/2020"
 
-import typing
 import functools
-from tomwer.utils import docstring
+import logging
+import typing
+
 from silx.gui import qt
+from silx.gui.dialog.DataFileDialog import DataFileDialog
+from silx.utils.enum import Enum as _Enum
+
+from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSliceMode
 from tomwer.core.process.reconstruction.nabu.utils import (
-    _NabuStages,
-    _NabuReconstructionMethods,
     _NabuFBPFilterType,
     _NabuPaddingType,
+    _NabuReconstructionMethods,
+    _NabuStages,
 )
-from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSliceMode
 from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
 from tomwer.gui.utils.inputwidget import SelectionLineEdit
-from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel
-from tomwer.gui.utils.scrollarea import QDoubleSpinBoxIgnoreWheel
-from tomwer.gui.utils.scrollarea import QSpinBoxIgnoreWheel
-from silx.utils.enum import Enum as _Enum
-from silx.gui.dialog.DataFileDialog import DataFileDialog
-
-import logging
+from tomwer.gui.utils.scrollarea import (
+    QComboBoxIgnoreWheel,
+    QDoubleSpinBoxIgnoreWheel,
+    QSpinBoxIgnoreWheel,
+)
+from tomwer.utils import docstring
 
 _logger = logging.getLogger(__name__)
 
@@ -543,15 +546,15 @@ class _NabuReconstructionConfig(qt.QWidget, _NabuStageConfigBase):
         else:
             return None
 
-    def setFBPFilterType(self, filter):
-        if type(filter) is str and filter.lower() == "none":
-            filter = None
-        if filter is None:
+    def setFBPFilterType(self, filter_type):
+        if type(filter_type) is str and filter_type.lower() == "none":
+            filter_type = None
+        if filter_type is None:
             self._fbpFilterCB.setChecked(False)
         else:
             self._fbpFilterCB.setChecked(True)
-            filter = _NabuFBPFilterType(filter)
-            filter_index = self._fbpFilterType.findText(filter.value)
+            filter_type = _NabuFBPFilterType(filter_type)
+            filter_index = self._fbpFilterType.findText(filter_type.value)
             self._fbpFilterType.setCurrentIndex(filter_index)
 
     def getFBPPaddingType(self) -> _NabuPaddingType:
@@ -778,33 +781,33 @@ class _SubRegionEditor(qt.QObject):
         else:
             return None
 
-    def setSubRegionMin(self, min: typing.Union[None, int]) -> None:
+    def setSubRegionMin(self, sub_region_min: typing.Union[None, int]) -> None:
         """
 
         :param min: if min is None or -1 wr will expand it to - infinity
         """
-        if min in (-1, 0):
-            min = None
-        if min is None:
+        if sub_region_min in (-1, 0):
+            sub_region_min = None
+        if sub_region_min is None:
             self._minCB.setChecked(False)
         else:
             self._minCB.setChecked(True)
-            self._minQLE.setText(str(min))
+            self._minQLE.setText(str(sub_region_min))
 
-    def setSubRegionMax(self, max) -> None:
+    def setSubRegionMax(self, sub_region_max) -> None:
         """
 
         :param max: if max is None or -1 wr will expand it to infinity
         """
-        if type(max) is str:
-            max = int(max)
-        if max == -1:
-            max = None
-        if max is None:
+        if type(sub_region_max) is str:
+            sub_region_max = int(sub_region_max)
+        if sub_region_max == -1:
+            sub_region_max = None
+        if sub_region_max is None:
             self._maxCB.setChecked(False)
         else:
             self._maxCB.setChecked(True)
-            self._maxQLE.setText(str(max))
+            self._maxQLE.setText(str(sub_region_max))
 
     def getSubRegion(self) -> tuple:
         """
@@ -814,14 +817,18 @@ class _SubRegionEditor(qt.QObject):
         """
         return self.getSubRegionMin(), self.getSubRegionMax()
 
-    def setSubRegion(self, min: typing.Union[None, int], max: typing.Union[None, int]):
+    def setSubRegion(
+        self,
+        sub_region_min: typing.Union[None, int],
+        sub_region_max: typing.Union[None, int],
+    ):
         """
 
         :param tuple min:
         :param tuple max:
         """
-        self.setSubRegionMin(min)
-        self.setSubRegionMax(max)
+        self.setSubRegionMin(sub_region_min)
+        self.setSubRegionMax(sub_region_max)
 
     def _signalConfChanged(self, param):
         self.sigConfChanged.emit(param)

tomwer/gui/reconstruction/nabu/nabuflow.py

@@ -27,14 +27,17 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "04/03/2019"
 
+import functools
+import typing
+
 from silx.gui import qt
+
+from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
 from tomwer.gui import icons
-from ...utils.flow import FlowDirection, FlowCanvas
 from tomwer.gui.utils.illustrations import _IllustrationWidget
 from tomwer.utils import docstring
-from tomwer.core.process.reconstruction.nabu.utils import _NabuStages
-import functools
-import typing
+
+from ...utils.flow import FlowCanvas, FlowDirection
 
 
 class NabuFlowControl(qt.QWidget):

tomwer/gui/reconstruction/nabu/slices.py

@@ -27,28 +27,31 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "04/03/2019"
 
-from silx.gui import qt
-from ...utils.flow import FlowDirection
-from .nabuconfig import NabuConfiguration
+import logging
+
 from nabu.pipeline.config import get_default_nabu_config
 from nabu.pipeline.fullfield.nabu_config import (
     nabu_config as nabu_fullfield_default_config,
 )
-from tomwer.core.process.reconstruction.nabu.utils import _NabuMode, ConfigurationLevel
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowArea
-from tomoscan.scanbase import _FOV
+from silx.gui import icons as silx_icons
+from silx.gui import qt
 from silx.utils.enum import Enum as _Enum
+from tomoscan.scanbase import _FOV
+
+from tomwer.core.process.reconstruction.nabu.utils import ConfigurationLevel, _NabuMode
+from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui import icons as tomwer_icons
+from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowArea
+from tomwer.gui.utils.buttons import PadlockButton
+
+from ...utils.flow import FlowDirection
 from .action import (
     BasicConfigurationAction,
     ExpertConfigurationAction,
     FilterAction,
     MinimalisticConfigurationAction,
 )
-from silx.gui import icons as silx_icons
-from tomwer.gui.utils.buttons import PadlockButton
-import logging
+from .nabuconfig import NabuConfiguration
 
 _logger = logging.getLogger(__name__)
 
@@ -317,6 +320,7 @@ class NabuWindow(qt.QMainWindow):
 
     def _saveParameters(self):
         from nabu.pipeline.config import generate_nabu_configfile
+
         from tomwer.core.process.reconstruction.nabu.nabuslices import (
             interpret_tomwer_configuration,
         )

tomwer/gui/reconstruction/nabu/slurm.py

@@ -29,6 +29,7 @@ __date__ = "11/10/2021"
 
 
 from silx.gui import qt
+
 from tomwer.core.settings import SlurmSettings
 from tomwer.core.utils.slurm import is_slurm_available
 

tomwer/gui/reconstruction/nabu/volume.py

@@ -28,23 +28,25 @@ __license__ = "MIT"
 __date__ = "04/08/2020"
 
 
-from asyncio.log import logger
 import typing
+from asyncio.log import logger
+
 from silx.gui import qt
+
 from tomwer.core.process.reconstruction.nabu.utils import (
     ConfigurationLevel,
     _NabuStages,
 )
+from tomwer.gui import icons
 from tomwer.gui.reconstruction.nabu.action import (
     BasicConfigurationAction,
     ExpertConfigurationAction,
     MinimalisticConfigurationAction,
 )
 from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
-from tomwer.gui import icons
 from tomwer.gui.reconstruction.nabu.nabuconfig.output import (
-    QNabuFileFormatComboBox,
     NabuOutputLocationWidget,
+    QNabuFileFormatComboBox,
 )
 
 

tomwer/gui/reconstruction/normalization/intensity.py

@@ -34,23 +34,24 @@ __license__ = "MIT"
 __date__ = "23/06/2021"
 
 
+import typing
+import weakref
+
 from silx.gui import qt
-from silx.io.url import DataUrl
-from silx.gui.plot.items.roi import RectangleROI
-from silx.gui.plot.items.roi import HorizontalRangeROI
-from silx.gui.plot.tools.roi import RegionOfInterestManager
 from silx.gui.dialog.DataFileDialog import DataFileDialog
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomwer.gui.visualization.dataviewer import DataViewer
-from tomwer.gui.reconstruction.scores.control import ControlWidget
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.gui.visualization.sinogramviewer import SinogramViewer as _SinogramViewer
+from silx.gui.plot.items.roi import HorizontalRangeROI, RectangleROI
+from silx.gui.plot.tools.roi import RegionOfInterestManager
+from silx.io.url import DataUrl
+from tomoscan.normalization import Method
+
 from tomwer.core.process.reconstruction.normalization import params as _normParams
 from tomwer.core.process.reconstruction.normalization.params import _ValueSource
-from tomoscan.normalization import Method
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.gui.reconstruction.scores.control import ControlWidget
 from tomwer.gui.utils.buttons import PadlockButton
-import weakref
-import typing
+from tomwer.gui.visualization.dataviewer import DataViewer
+from tomwer.gui.visualization.sinogramviewer import SinogramViewer as _SinogramViewer
 
 
 class SinoNormWindow(qt.QMainWindow):
@@ -907,7 +908,7 @@ class _NormIntensityDatasetWidget(qt.QWidget):
         elif self.getMode() is _normParams._DatasetScope.GLOBAL:
             file_ = self.getGlobalFilePath()
         else:
-            raise ValueError("{} is not handled".format(self.getMode()))
+            raise ValueError(f"{self.getMode()} is not handled")
 
         dialog = DataFileDialog()
         dialog.selectFile(file_)