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

tomwer/gui/visualization/diffviewer/diffviewer.py

@@ -34,21 +34,23 @@ __date__ = "23/03/2022"
 import functools
 import logging
 import os
+
 import numpy
 from processview.core.dataset import DatasetIdentifier
+from silx.gui import icons as silx_icons
+from silx.gui import qt
+from silx.io.url import DataUrl
+from silx.utils.enum import Enum as _Enum
+
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.core.utils.image import shift_img
-from tomwer.gui.settings import Y_AXIS_DOWNWARD
-from tomwer.gui.utils.completer import UrlCompleterDialog
-from tomwer.io.utils import get_slice_data
 from tomwer.gui.qfolderdialog import QDataDialog
 from tomwer.gui.reconstruction.axis.CompareImages import CompareImages as _CompareImages
+from tomwer.gui.settings import Y_AXIS_DOWNWARD
+from tomwer.gui.utils.completer import UrlCompleterDialog
 from tomwer.gui.visualization.diffviewer.shiftwidget import TwoFramesShiftTab
-from silx.gui import qt
-from silx.io.url import DataUrl
-from silx.utils.enum import Enum as _Enum
-from silx.gui import icons as silx_icons
+from tomwer.io.utils import get_slice_data
 
 _logger = logging.getLogger(__name__)
 
@@ -60,14 +62,14 @@ class CompareImages(_CompareImages):
         self.getPlot().setPanWithArrowKeys(False)
         self._firstVisible = True
 
-    def setVisible(self, bool):
+    def setVisible(self, visible):
         if self._firstVisible:
             # hack to enforce matplotlib to replot the widget.
             # because it looks like it is missing to find the correct viewport
             # when not visible
             self.getPlot().resetZoom()
             self._firstVisible = False
-        super().setVisible(bool)
+        super().setVisible(visible)
 
 
 class _FrameSelector(qt.QWidget):
@@ -166,7 +168,7 @@ class _FrameSelector(qt.QWidget):
         elif type_selected == self.FrameType.RECON_SLICES:
             urls = self._scan.get_reconstructions_urls()
         else:
-            raise ValueError("Type {} not managed".format(type_selected))
+            raise ValueError(f"Type {type_selected} not managed")
         urls = sorted(urls, key=lambda url: url.path())
         for url in urls:
             if url.data_slice() is not None:
@@ -269,7 +271,7 @@ class _FramesSelector(qt.QWidget):
 
     def addScan(self, scan):
         if not isinstance(scan, TomwerScanBase):
-            raise TypeError("scan should be an instance of {}".format(TomwerScanBase))
+            raise TypeError(f"scan should be an instance of {TomwerScanBase}")
         self._leftScanCB.addScan(scan.get_identifier())
         self._rightScanCB.addScan(scan.get_identifier())
 
@@ -319,9 +321,7 @@ class _FramesSelector(qt.QWidget):
                 scans = ScanFactory.create_scan_objects(scan_path=folder)
             except Exception as e:
                 _logger.error(
-                    "cannot create scan instances from {}. Error is {}".format(
-                        folder, e
-                    )
+                    f"cannot create scan instances from {folder}. Error is {e}"
                 )
             else:
                 for scan in scans:
@@ -445,7 +445,7 @@ class DiffFrameViewer(qt.QMainWindow):
             if data.ndim == 3 and data.shape[0] == 1:
                 data = data.reshape((data.shape[1], data.shape[2]))
             else:
-                _logger.error("Cannot display {}. Should be 2D".format(url.path()))
+                _logger.error(f"Cannot display {url.path()}. Should be 2D")
                 return
 
         if self.isFrameALRFlip():
@@ -478,7 +478,7 @@ class DiffFrameViewer(qt.QMainWindow):
             if data.ndim == 3 and data.shape[0] == 1:
                 data = data.reshape((data.shape[1], data.shape[2]))
             else:
-                _logger.error("Cannot display {}. Should be 2D".format(url.path()))
+                _logger.error(f"Cannot display {url.path()}. Should be 2D")
                 return
         if self.isFrameBLRFlip():
             data = numpy.fliplr(data)
@@ -548,10 +548,7 @@ class _ScanComboBox(qt.QWidget):
         try:
             scan = DatasetIdentifier.recreate_dataset(dataset_id)
         except Exception as e:
-            _logger.error(
-                "Fail to recreate dataset from {}. Reason is {}."
-                "".format(str(dataset_id), e)
-            )
+            _logger.error(f"Fail to recreate dataset from {dataset_id}. Reason is {e}.")
             return None
         else:
             return scan

tomwer/gui/visualization/diffviewer/shiftwidget.py

@@ -31,9 +31,11 @@ __license__ = "MIT"
 __date__ = "07/12/2021"
 
 
+import sys
+
 from silx.gui import qt
 from silx.utils.enum import Enum as _Enum
-import sys
+
 from tomwer.utils import docstring
 
 

tomwer/gui/visualization/nxtomometadata.py

@@ -1,4 +1,5 @@
 from silx.gui import qt
+
 from tomwer.gui.edit.nxtomoeditor import NXtomoEditor as _NXtomoEditor
 
 

tomwer/gui/visualization/reconstructionparameters.py

@@ -28,12 +28,14 @@ __license__ = "MIT"
 __date__ = "31/03/2021"
 
 
+import os
+
 from silx.gui import qt
 from silx.io.url import DataUrl
 from silx.io.utils import h5py_read_dataset
-from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 from tomoscan.io import HDF5File
-import os
+
+from tomwer.core.utils.char import BETA_CHAR, DELTA_CHAR
 
 
 class ReconstructionParameters(qt.QWidget):
@@ -99,8 +101,7 @@ class ReconstructionParameters(qt.QWidget):
             url = DataUrl(path=url)
         else:
             raise TypeError(
-                "url should be a DataUrl or a str representing"
-                "an url and not {}".format(type(url))
+                f"url should be a DataUrl or a str representing an url and not {type(url)}"
             )
         for func in (
             self._setMethod,
@@ -120,10 +121,10 @@ class ReconstructionParameters(qt.QWidget):
             func(url)
 
     @staticmethod
-    def _decode_nabu_str(input):
-        if hasattr(input, "decode"):
-            input = input.decode("UTF-8")
-        return input
+    def _decode_nabu_str(input_str):
+        if hasattr(input_str, "decode"):
+            input_str = input_str.decode("UTF-8")
+        return input_str
 
     def _setMethod(self, url):
         def get_method_value():
@@ -186,7 +187,7 @@ class ReconstructionParameters(qt.QWidget):
 
         value = self._decode_nabu_str(get_distance_value())
         if value is not None:
-            value = "{:.2}".format(float(value))
+            value = f"{value:.2}"
         self._distanceQLE.setText(value if value is not None else "")
 
     def _setPixelSize(self, url):
@@ -206,7 +207,7 @@ class ReconstructionParameters(qt.QWidget):
 
         value = self._decode_nabu_str(get_pixel_size_value())
         if value is not None:
-            value = "{:.8}".format(float(value))
+            value = f"{float(value):.8}"
         self._pixelSizeQLE.setText(value if value is not None else "")
 
     def _setCor(self, url):
@@ -222,7 +223,7 @@ class ReconstructionParameters(qt.QWidget):
 
         value = self._decode_nabu_str(get_cor_value())
         if value not in (None, "None", "none"):
-            value = "{:.4f}".format(float(value))
+            value = f"{float(value):.4f}"
         self._corQLE.setText(value if value is not None else "")
 
     def _setPaddingType(self, url):
@@ -369,4 +370,4 @@ class ReconstructionParameters(qt.QWidget):
         if nabu_version is not None:
             software = "nabu"
             software_version = nabu_version
-        self._softwareVersionQLE.setText("{} ({})".format(software, software_version))
+        self._softwareVersionQLE.setText(f"{software} ({software_version})")

tomwer/gui/visualization/scanoverview.py

@@ -28,11 +28,13 @@ __license__ = "MIT"
 __date__ = "31/03/2021"
 
 
-from silx.gui import qt
-from tomwer.core.scan.scanbase import TomwerScanBase
-import weakref
 import logging
+import weakref
+
+from silx.gui import qt
+
 from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.scanbase import TomwerScanBase
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/visualization/sinogramviewer.py

@@ -31,11 +31,12 @@ __license__ = "MIT"
 __date__ = "26/03/2020"
 
 
-from silx.gui import qt
-from silx.gui.plot.ImageStack import _PlotWithWaitingLabel
 import logging
 import weakref
 
+from silx.gui import qt
+from silx.gui.plot.ImageStack import _PlotWithWaitingLabel
+
 from tomwer.gui.settings import Y_AXIS_DOWNWARD
 
 _logger = logging.getLogger(__name__)

tomwer/gui/visualization/test/test_dataviewer.py

@@ -29,8 +29,10 @@ __date__ = "30/07/2020"
 
 
 import unittest
-from silx.gui.utils.testutils import TestCaseQt
+
 from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
 from tomwer.gui.visualization.dataviewer import DataViewer, ImageStack
 
 

tomwer/gui/visualization/test/test_diffviewer.py

@@ -28,15 +28,17 @@ __license__ = "MIT"
 __date__ = "21/06/2021"
 
 
+import logging
+import os
+import shutil
+import tempfile
+import unittest
+
 from silx.gui import qt
-from tomwer.core.utils.scanutils import MockHDF5
 from silx.gui.utils.testutils import TestCaseQt
+
+from tomwer.core.utils.scanutils import MockHDF5
 from tomwer.gui.visualization.diffviewer import DiffFrameViewer
-import unittest
-import logging
-import tempfile
-import shutil
-import os
 
 logging.disable(logging.INFO)
 

tomwer/gui/visualization/test/test_nx_tomo_metadata_viewer.py

@@ -1,12 +1,14 @@
 import os
-import pytest
+
 import numpy
+import pytest
+from nxtomomill.nexus.nxtomo import NXtomo
+from silx.gui import qt
 from tomoscan.esrf.scan.hdf5scan import ImageKey
+
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
-from nxtomomill.nexus.nxtomo import NXtomo
 from tomwer.tests.conftest import qtapp  # noqa F401
-from silx.gui import qt
 
 
 def test_nx_editor(

tomwer/gui/visualization/test/test_reconstruction_parameters.py

@@ -28,12 +28,14 @@ __license__ = "MIT"
 __date__ = "15/12/2021"
 
 
+import os
+import shutil
 import tempfile
-from silx.gui.utils.testutils import TestCaseQt
+
 from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
 from silx.io.url import DataUrl
-import shutil
-import os
+
 from tomwer.core.utils import scanutils
 from tomwer.gui.visualization.reconstructionparameters import ReconstructionParameters
 

tomwer/gui/visualization/test/test_sinogramviewer.py

@@ -28,17 +28,18 @@ __license__ = "MIT"
 __date__ = "22/01/2017"
 
 
-from silx.gui.utils.testutils import SignalListener
-from tomwer.gui.visualization import sinogramviewer
-from silx.gui import qt
-from tomwer.core.utils.scanutils import MockHDF5
-from silx.gui.utils.testutils import TestCaseQt
-import unittest
 import logging
-import time
-import tempfile
-import shutil
 import os
+import shutil
+import tempfile
+import time
+import unittest
+
+from silx.gui import qt
+from silx.gui.utils.testutils import SignalListener, TestCaseQt
+
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.gui.visualization import sinogramviewer
 
 logging.disable(logging.INFO)
 

tomwer/gui/visualization/test/test_stacks.py

@@ -26,20 +26,22 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "16/06/2021"
 
+import logging
 import os
 import shutil
 import tempfile
+import time
+import weakref
+
 import numpy
-from tomwer.core.utils.scanutils import MockHDF5
-from tomwer.gui.stacks import SliceStack, RadioStack
+import pytest
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
-import logging
-import time
-import pytest
 from tomoscan.esrf.volume.edfvolume import EDFVolume
+
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.gui.stacks import RadioStack, SliceStack
 from tomwer.tests.utils import skip_gui_test
-import weakref
 
 logging.disable(logging.INFO)
 

tomwer/gui/visualization/test/test_volumeviewer.py

@@ -28,17 +28,19 @@ __license__ = "MIT"
 __date__ = "21/06/2021"
 
 
+import logging
+import os
+import shutil
+import tempfile
+import unittest
+
+import numpy
 from silx.gui import qt
-from tomwer.core.utils.scanutils import MockHDF5
 from silx.gui.utils.testutils import TestCaseQt
-from tomwer.gui.visualization.volumeviewer import VolumeViewer
 from tomoscan.esrf.volume.hdf5volume import HDF5Volume
-import numpy
-import unittest
-import logging
-import tempfile
-import shutil
-import os
+
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.gui.visualization.volumeviewer import VolumeViewer
 
 logging.disable(logging.INFO)
 

tomwer/gui/visualization/tomoobjoverview.py

@@ -1,10 +1,13 @@
-from .volumeoverview import VolumeOverviewWidget
-from .scanoverview import ScanOverviewWidget
+from typing import Optional
+
 from silx.gui import qt
+
+from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.tomwer_object import TomwerObject
 from tomwer.core.volume.volumebase import TomwerVolumeBase
-from tomwer.core.scan.scanbase import TomwerScanBase
-from typing import Optional
+
+from .scanoverview import ScanOverviewWidget
+from .volumeoverview import VolumeOverviewWidget
 
 
 class TomoObjOverview(qt.QWidget):

tomwer/gui/visualization/volumeoverview.py

@@ -1,8 +1,10 @@
+import logging
+from typing import Optional
+
 from silx.gui import qt
-from tomwer.core.volume.volumebase import TomwerVolumeBase
 from tomoscan.identifier import VolumeIdentifier
-from typing import Optional
-import logging
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/visualization/volumeviewer.py

@@ -28,25 +28,26 @@ __license__ = "MIT"
 __date__ = "05/08/2020"
 
 
+import logging
+import os
+import weakref
+
+import numpy
+import numpy.lib.npyio
+import silx
 from silx.gui import qt
-from tomoscan.volumebase import VolumeBase
-from tomoscan.identifier import VolumeIdentifier
-from tomoscan.esrf.volume.hdf5volume import HDF5Volume
-from tomoscan.factory import Factory
+from silx.gui.colors import Colormap
 from silx.gui.data.DataViewerFrame import DataViewerFrame
+from silx.gui.data.DataViews import IMAGE_MODE, DataViewHooks
 from silx.gui.dialog.ColormapDialog import ColormapDialog
-from silx.gui.data.DataViews import DataViewHooks
-from silx.gui.data.DataViews import IMAGE_MODE
-import os
+from tomoscan.esrf.volume.hdf5volume import HDF5Volume
+from tomoscan.factory import Factory
+from tomoscan.identifier import VolumeIdentifier
+from tomoscan.volumebase import VolumeBase
+
 from tomwer.core.scan.scanbase import TomwerScanBase
-import logging
 from tomwer.core.utils.ftseriesutils import get_vol_file_shape
-import weakref
 from tomwer.gui.visualization.reconstructionparameters import ReconstructionParameters
-import silx
-from silx.gui.colors import Colormap
-import numpy
-import numpy.lib.npyio
 
 _logger = logging.getLogger(__name__)
 
@@ -292,7 +293,7 @@ class VolumeViewer(qt.QMainWindow):
             return
 
         elif len(scan.latest_vol_reconstructions) == 0:
-            _logger.warning("No reconstructed volume for {}".format(scan))
+            _logger.warning(f"No reconstructed volume for {scan}")
             self.clear()
             self._infoWidget.setScan(scan)
         else:

tomwer/io/utils/__init__.py

@@ -1,5 +1,5 @@
-from .utils import get_slice_data  # noqa F401
-from .utils import get_default_directory  # noqa F401
 from .utils import format_stderr_stdout  # noqa F401
-from .utils import get_linked_files_with_vds  # noqa F401
+from .utils import get_default_directory  # noqa F401
 from .utils import get_linked_files_with_entry  # noqa F401
+from .utils import get_linked_files_with_vds  # noqa F401
+from .utils import get_slice_data  # noqa F401

tomwer/io/utils/h5pyutils.py

@@ -32,9 +32,10 @@ __date__ = "22/04/2021"
 
 
 import contextlib
+
+import h5py
 from silx.io.url import DataUrl
 from tomoscan.io import HDF5File
-import h5py
 
 
 class _BaseReader(contextlib.AbstractContextManager):

tomwer/io/utils/utils.py

@@ -31,15 +31,17 @@ __license__ = "MIT"
 __date__ = "07/09/2020"
 
 
-import numpy.lib.npyio
+import logging
 import os
+
+import h5py
+import numpy.lib.npyio
+from PIL import Image
+from tomoscan.esrf import has_glymur
 from tomoscan.esrf.scan.utils import get_data as tomoscan_get_data
 from tomoscan.io import HDF5File
+
 from tomwer.core.utils import ftseriesutils
-from PIL import Image
-import logging
-import h5py
-from tomoscan.esrf import has_glymur
 
 try:
     import tifffile  # noqa #F401 needed for later possible lazy loading
@@ -106,47 +108,41 @@ def _loadVol(url):
 
     if not os.path.exists(rawFile):
         data = None
-        mess = "Can't find raw data file %s associated with %s" % (rawFile, infoFile)
+        mess = f"Can't find raw data file {rawFile} associated with {infoFile}"
         _logger.warning(mess)
     elif not os.path.exists(infoFile):
-        mess = "Can't find info file %s associated with %s" % (infoFile, rawFile)
+        mess = f"Can't find info file {infoFile} associated with {rawFile}"
         _logger.warning(mess)
         data = None
     else:
         shape = ftseriesutils.get_vol_file_shape(infoFile)
         if None in shape:
-            _logger.warning("Fail to retrieve data shape for %s." % infoFile)
+            _logger.warning(f"Fail to retrieve data shape for {infoFile}.")
             data = None
         else:
             try:
                 numpy.zeros(shape)
             except MemoryError:
                 data = None
-                _logger.warning(
-                    "Raw file %s is to large for being " "readed %s" % rawFile
-                )
+                _logger.warning(f"Raw file {rawFile} is to large for being readed")
             else:
                 data = numpy.fromfile(rawFile, dtype=numpy.float32, count=-1, sep="")
                 try:
                     data = data.reshape(shape)
                 except ValueError:
                     _logger.warning(
-                        "unable to fix shape for raw file %s. "
-                        "Look for information in %s"
-                        "" % (rawFile, infoFile)
+                        f"unable to fix shape for raw file {rawFile}. Look for information in {infoFile}"
                     )
                     try:
                         sqr = int(numpy.sqrt(len(data)))
                         shape = (1, sqr, sqr)
                         data = data.reshape(shape)
                     except ValueError:
-                        _logger.info("deduction of shape size for %s failed" % rawFile)
+                        _logger.info(f"deduction of shape size for {rawFile} failed")
                         data = None
                     else:
                         _logger.warning(
-                            "try deducing shape size for %s "
-                            "might be an incorrect "
-                            "interpretation" % rawFile
+                            f"try deducing shape size for {rawFile} might be an incorrect interpretation"
                         )
     if url.data_slice() is None:
         return data
@@ -179,9 +175,9 @@ def format_stderr_stdout(stdout, stderr, config=None):
     else:
         assert isinstance(config, dict)
     return (
-        "############# nabu ############## \nconfig: {}\n"
-        "------------- stderr -------------\n{}\n"
-        "------------- stdout -------------\n{}\n".format(config, s_err, s_out)
+        f"############# nabu ############## \nconfig: {config}\n"
+        f"------------- stderr -------------\n{s_err}\n"
+        f"------------- stdout -------------\n{s_out}\n"
     )
 
 

tomwer/resources/__init__.py

@@ -24,8 +24,8 @@
 # ###########################################################################*/
 
 
-import os
 import importlib
+import os
 import sys
 
 # pkg_resources is useful when this package is stored in a zip

tomwer/synctools/axis.py

@@ -27,9 +27,11 @@ __license__ = "MIT"
 __date__ = "03/05/2019"
 
 
+import logging
+
 from silx.gui import qt
+
 from tomwer.core.process.reconstruction.axis.params import AxisRP
-import logging
 
 logger = logging.getLogger(__name__)
 

tomwer/synctools/darkref.py

@@ -27,10 +27,11 @@ __license__ = "MIT"
 __date__ = "03/05/2019"
 
 
+import logging
+
 from silx.gui import qt
-from tomwer.core.process.reconstruction.darkref import params as dkrf
 
-import logging
+from tomwer.core.process.reconstruction.darkref import params as dkrf
 
 logger = logging.getLogger(__name__)
 

tomwer/synctools/datalistener.py

@@ -28,16 +28,20 @@ __license__ = "MIT"
 __date__ = "16/03/2020"
 
 
-from tomwer.core.process.control.datalistener.rpcserver import _BaseDataListenerThread
-from tomwer.core.process.control.datalistener.rpcserver import BlissAcquisition
-from tomwer.core.process.control.datalistener.rpcserver import TangoAcquisitionStatus
+import logging
+import time
 from collections import namedtuple
 from datetime import datetime
+from multiprocessing import Lock, Manager
+
 from silx.gui import qt
+
+from tomwer.core.process.control.datalistener.rpcserver import (
+    BlissAcquisition,
+    TangoAcquisitionStatus,
+    _BaseDataListenerThread,
+)
 from tomwer.utils import docstring
-import time
-from multiprocessing import Manager, Lock
-import logging
 
 _logger = logging.getLogger(__name__)
 

tomwer/synctools/datatransfert.py

@@ -29,9 +29,8 @@ __date__ = "28/01/2019"
 
 
 from silx.gui import qt
-from tomwer.core.process.control.scantransfer import (
-    ScanTransfer as FolderTransfertP,
-)
+
+from tomwer.core.process.control.scantransfer import ScanTransfer as FolderTransfertP
 from tomwer.core.scan.scanbase import TomwerScanBase