tomwer 1.1.0rc7__py3-none-any.whl → 1.2.0a0__py3-none-any.whl

tomwer/gui/reconstruction/test/test_axis.py

@@ -27,22 +27,23 @@ __license__ = "MIT"
 __date__ = "16/06/2021"
 
 
-from tomwer.gui.reconstruction.axis import AxisWindow
-from tomwer.gui.reconstruction.axis.radioaxis import _ManualFramesSelection
-from tomwer.tests.utils import skip_gui_test
-from tomwer.tests.utils import UtilsTest
-from tomwer.core.process.reconstruction.axis.mode import AxisMode
-from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.synctools.axis import QAxisRP
-from silx.gui.utils.testutils import TestCaseQt
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from silx.gui import qt
-import numpy.random
-import pytest
-import tempfile
 import os
 import shutil
+import tempfile
+
 import h5py
+import numpy.random
+import pytest
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from tomwer.core.process.reconstruction.axis.mode import AxisMode
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.gui.reconstruction.axis import AxisWindow
+from tomwer.gui.reconstruction.axis.radioaxis import _ManualFramesSelection
+from tomwer.synctools.axis import QAxisRP
+from tomwer.tests.utils import UtilsTest, skip_gui_test
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")

tomwer/gui/reconstruction/test/test_lamino.py

@@ -31,12 +31,13 @@ import os
 import shutil
 import tempfile
 import unittest
+
 import pytest
 from silx.gui import qt
+
 from tomwer.core import settings
 from tomwer.gui.reconstruction.lamino.tofu import TofuWindow
-from tomwer.tests.utils import UtilsTest
-from tomwer.tests.utils import skip_gui_test
+from tomwer.tests.utils import UtilsTest, skip_gui_test
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")

tomwer/gui/reconstruction/test/test_nabu.py

@@ -28,21 +28,23 @@ __date__ = "05/02/2020"
 
 
 import os
+
+import pytest
 from silx.gui import qt
-from tomwer.tests.utils import skip_gui_test
-from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowControl
+from silx.gui.utils.testutils import TestCaseQt
+
+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,
     _RingCorrectionMethod,
 )
-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.gui.reconstruction.nabu.nabuflow import NabuFlowControl
 from tomwer.gui.reconstruction.nabu.volume import NabuVolumeWidget
-from silx.gui.utils.testutils import TestCaseQt
-import pytest
+from tomwer.tests.utils import skip_gui_test
 
 
 class ProcessClass:

tomwer/gui/reconstruction/test/test_saaxis.py

@@ -27,26 +27,28 @@ __license__ = "MIT"
 __date__ = "03/02/2021"
 
 
-from tomwer.tests.utils import skip_gui_test
-from tomwer.gui.reconstruction.saaxis.dimensionwidget import DimensionWidget
-from tomoscan.unitsystem import metricsystem
+import os
+import shutil
+import tempfile
+
+import h5py
+import numpy
+import pytest
+from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
-from tomwer.core.utils.scanutils import MockHDF5
-from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow
+from silx.io.url import DataUrl
+from tomoscan.unitsystem import metricsystem
+
 from tomwer.core.process.reconstruction.saaxis.params import (
-    SAAxisParams,
     ReconstructionMode,
+    SAAxisParams,
 )
 from tomwer.core.process.reconstruction.scores import ComputedScore
 from tomwer.core.process.reconstruction.scores.params import ScoreMethod
-from silx.io.url import DataUrl
-from silx.gui import qt
-import pytest
-import numpy
-import shutil
-import tempfile
-import os
-import h5py
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.gui.reconstruction.saaxis.dimensionwidget import DimensionWidget
+from tomwer.gui.reconstruction.saaxis.saaxis import SAAxisWindow
+from tomwer.tests.utils import skip_gui_test
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
@@ -127,7 +129,7 @@ class TestSAAxisWindow(TestCaseQt):
         self._cor_scores = {}
 
         for i in range(self._N_OUTPUT_URLS):
-            output_file = os.path.join(self.folder, "recons_{}.h5".format(i))
+            output_file = os.path.join(self.folder, f"recons_{i}.h5")
             with h5py.File(output_file, mode="a") as h5f:
                 h5f["data"] = numpy.random.random(100 * 100).reshape(100, 100)
                 url = DataUrl(file_path=output_file, data_path="data", scheme="silx")

tomwer/gui/reconstruction/test/test_sadeltabeta.py

@@ -27,21 +27,23 @@ __license__ = "MIT"
 __date__ = "09/06/2021"
 
 
-from tomwer.tests.utils import skip_gui_test
-from silx.gui.utils.testutils import TestCaseQt
-from tomwer.core.utils.scanutils import MockHDF5
-from tomwer.gui.reconstruction.sadeltabeta import SADeltaBetaWindow
-from tomwer.core.process.reconstruction.sadeltabeta.params import SADeltaBetaParams
-from tomwer.core.process.reconstruction.scores.params import ScoreMethod
-from tomwer.core.process.reconstruction.scores import ComputedScore
-from silx.io.url import DataUrl
-from silx.gui import qt
-import pytest
-import numpy
+import os
 import shutil
 import tempfile
-import os
+
 import h5py
+import numpy
+import pytest
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+from silx.io.url import DataUrl
+
+from tomwer.core.process.reconstruction.sadeltabeta.params import SADeltaBetaParams
+from tomwer.core.process.reconstruction.scores import ComputedScore
+from tomwer.core.process.reconstruction.scores.params import ScoreMethod
+from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.gui.reconstruction.sadeltabeta import SADeltaBetaWindow
+from tomwer.tests.utils import skip_gui_test
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
@@ -58,7 +60,7 @@ class TestSADeltaBetaWindow(TestCaseQt):
         self._cor_scores = {}
 
         for i in range(self._N_OUTPUT_URLS):
-            output_file = os.path.join(self.folder, "recons_{}.h5".format(i))
+            output_file = os.path.join(self.folder, f"recons_{i}.h5")
             with h5py.File(output_file, mode="a") as h5f:
                 h5f["data"] = numpy.random.random(100 * 100).reshape(100, 100)
                 url = DataUrl(file_path=output_file, data_path="data", scheme="silx")

tomwer/gui/samplemoved/__init__.py

@@ -30,16 +30,17 @@ __license__ = "MIT"
 __date__ = "19/03/2018"
 
 
-from collections import OrderedDict
+import logging
 import weakref
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.gui.samplemoved.selectiontable import AngleSelectionTable
-from tomoscan.esrf.scan.utils import get_data
-from silx.gui import qt
-import silx.io.utils
+from collections import OrderedDict
+
 import silx.io.url
-import logging
+import silx.io.utils
+from silx.gui import qt
+from tomoscan.esrf.scan.utils import get_data
 
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.gui.samplemoved.selectiontable import AngleSelectionTable
 from tomwer.gui.settings import Y_AXIS_DOWNWARD
 
 _logger = logging.getLogger(__name__)

tomwer/gui/samplemoved/selectiontable.py

@@ -30,13 +30,15 @@ __license__ = "MIT"
 __date__ = "17/08/2021"
 
 
+import functools
+import logging
 import os
 from collections import OrderedDict
-import functools
+
 from silx.gui import qt
 from silx.io.url import DataUrl
+
 from tomwer.gui.imagefromfile import FileWithImage
-import logging
 
 logger = logging.getLogger(__name__)
 

tomwer/gui/stackplot.py

@@ -28,24 +28,25 @@ __author__ = ["P. Paleo", "H. Payno"]
 __license__ = "MIT"
 __date__ = "24/05/2016"
 
+import functools
+import logging
+import os
+import time
+from collections import OrderedDict, namedtuple
+from typing import Iterable, Optional
+
+import numpy
 from silx.gui import qt
 from silx.gui.plot import Plot2D
-from . import utils
-from tomwer.gui import settings
-import numpy
-import os
-from collections import OrderedDict
-import tomwer.resources
-from .imagefromfile import ImageFromFile, FileWithImage, _Image
 from silx.gui.plot.actions import PlotAction
 from silx.gui.plot.actions.control import YAxisInvertedAction
 from silx.io.url import DataUrl
-import logging
-from tomwer.gui import icons
-import functools
-import time
-from collections import namedtuple
-from typing import Iterable, Optional
+
+import tomwer.resources
+from tomwer.gui import icons, settings
+
+from . import utils
+from .imagefromfile import FileWithImage, ImageFromFile, _Image
 
 logger = logging.getLogger(__name__)
 

tomwer/gui/stacks.py

@@ -30,17 +30,19 @@ __license__ = "MIT"
 __date__ = "19/03/2018"
 
 
+import logging
+from collections import OrderedDict
 from typing import Union
+
+import h5py
 from silx.gui import qt
-from tomwer.gui.stackplot import _QImageFileStackPlot
-from collections import OrderedDict
-from tomwer.gui.qfolderdialog import QDataDialog
+from tomoscan.factory import Factory
+from tomoscan.identifier import VolumeIdentifier
+
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
-from tomoscan.identifier import VolumeIdentifier
-from tomoscan.factory import Factory
-import logging
-import h5py
+from tomwer.gui.qfolderdialog import QDataDialog
+from tomwer.gui.stackplot import _QImageFileStackPlot
 
 _logger = logging.getLogger(__name__)
 
@@ -131,8 +133,8 @@ class _ImageStack(qt.QMainWindow):
         for scan in all_images:
             try:
                 oScanSlices = OrderedDict(sorted(all_images[scan].items()))
-                for slice in oScanSlices:
-                    ordered_imgs.append(all_images[scan][slice])
+                for scan_slice in oScanSlices:
+                    ordered_imgs.append(all_images[scan][scan_slice])
             except TypeError:
                 # in case algorithm could extract recons index
                 ordered_imgs = ordered_imgs + list(all_images[scan].values())

tomwer/gui/test/test_axis_gui.py

@@ -1,8 +1,9 @@
+import pytest
+from silx.gui.utils.testutils import TestCaseQt
+
 from tomwer.gui.reconstruction.axis.radioaxis import AxisTabWidget
 from tomwer.synctools.axis import QAxisRP
-from silx.gui.utils.testutils import TestCaseQt
 from tomwer.tests.utils import skip_gui_test
-import pytest
 
 
 @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
@@ -13,10 +14,10 @@ class TestGetNabuCorOpts(TestCaseQt):
         """
         axis_params = QAxisRP()
         widget = AxisTabWidget(recons_params=axis_params)
-        assert axis_params.get_nabu_cor_options_as_str() == "side='all'"
+        assert axis_params.get_nabu_cor_options_as_str() == "side='right'"
         widget._calculationWidget._corOpts.setText("low_pass=2")
         widget._calculationWidget._corOpts.editingFinished.emit()
-        assert axis_params.get_nabu_cor_options_as_str() == "side='all' ; low_pass=2"
+        assert axis_params.get_nabu_cor_options_as_str() == "side='right' ; low_pass=2"
         widget._calculationWidget._corOpts.setText("low_pass=2 ; high_pass=10")
         widget._calculationWidget._sideCB.setCurrentText("left")
         widget._calculationWidget._corOpts.editingFinished.emit()

tomwer/gui/test/test_qfolder_dialog.py

@@ -1,6 +1,7 @@
 import pytest
-from tomwer.tests.conftest import qtapp  # noqa F401
+
 from tomwer.gui.qfolderdialog import QDataDialog
+from tomwer.tests.conftest import qtapp  # noqa F401
 
 
 @pytest.mark.parametrize("multi_selection", (True, False))

tomwer/gui/utils/__init__.py

@@ -31,9 +31,9 @@ __license__ = "MIT"
 __date__ = "29/01/2020"
 
 
-import subprocess
 import logging
 import os
+import subprocess
 
 _logger = logging.getLogger(__name__)
 
@@ -76,10 +76,10 @@ def open_url_with_image_j(url):
         # for now we only manage the simple case of an edf file
         try:
             subprocess.call(["imagej", "-o", url.file_path()])
-        except Exception:
-            _logger.warning("Fail to open {}. Reason is {}".format(str(url), str()))
+        except Exception as e:
+            _logger.warning(f"Fail to open {url}. Reason is {e}")
     elif __image_j_from == "binary":
         try:
             subprocess.call([_IMAGE_J_BIN_PATH, url.file_path()])
-        except Exception:
-            _logger.warning("Fail to open {}. Reason is {}".format(str(url), str()))
+        except Exception as e:
+            _logger.warning(f"Fail to open {url}. Reason is {e}")

tomwer/gui/utils/buttons.py

@@ -32,6 +32,7 @@ __date__ = "03/10/2018"
 
 
 from silx.gui import qt
+
 from tomwer.gui import icons
 
 

tomwer/gui/utils/completer.py

@@ -32,6 +32,7 @@ __date__ = "23/03/2022"
 
 
 from typing import Optional
+
 from silx.gui import qt
 
 

tomwer/gui/utils/flow.py

@@ -28,10 +28,12 @@ __license__ = "MIT"
 __date__ = "04/03/2019"
 
 
+import functools
+from typing import Union
+
 from silx.gui import qt
 from silx.utils.enum import Enum as _Enum
-from typing import Union
-import functools
+
 from tomwer.gui import icons
 from tomwer.utils import docstring
 

tomwer/gui/utils/illustrations.py

@@ -32,6 +32,7 @@ __date__ = "28/09/2018"
 
 
 from silx.gui import qt
+
 from tomwer.gui import illustrations
 
 

tomwer/gui/utils/inputwidget.py

@@ -26,17 +26,16 @@ __authors__ = ["H.Payno"]
 __license__ = "MIT"
 __date__ = "16/08/2018"
 
-from silx.gui import qt
-from tomwer.gui import icons
-import numpy
 import logging
-
-from nxtomomill.io.config import (
-    TomoHDF5Config as HDF5Config,
-    TomoEDFConfig as EDFConfig,
-)
-from typing import Optional, Union
 import os
+from typing import Optional, Union
+
+import numpy
+from nxtomomill.io.config import TomoEDFConfig as EDFConfig
+from nxtomomill.io.config import TomoHDF5Config as HDF5Config
+from silx.gui import qt
+
+from tomwer.gui import icons
 from tomwer.gui.qlefilesystem import QLFileSystem
 from tomwer.io.utils import get_default_directory
 
@@ -98,7 +97,7 @@ class SelectionLineEdit(qt.QWidget):
                 _from, _to, _step = self._qLineEdit.text().split(":")
                 _from, _to, _step = float(_from), float(_to), float(_step)
                 if _from > _to:
-                    _logger.warning("to > from, invert %s and %s" % (_from, _to))
+                    _logger.warning(f"to > from, invert {_from} and {_to}")
                     tmp = _to
                     _to = _from
                     _from = tmp
@@ -399,18 +398,13 @@ class _ConfigFileSelector(qt.QWidget):
                 try:
                     self._load_config_file(cfg_file)
                 except Exception as e:
-                    mess = (
-                        "Fail to load nxtomomill configuration from {}. "
-                        "Error is {}".format(cfg_file, e)
-                    )
+                    mess = f"Fail to load nxtomomill configuration from {cfg_file}. Error is {e}"
                     _logger.warning(mess)
                     qt.QMessageBox.warning(
                         self, "Unable to read configuration from file", mess
                     )
                 else:
-                    _logger.info(
-                        "Will use {} as input configuration file." "".format(cfg_file)
-                    )
+                    _logger.info(f"Will use {cfg_file} as input configuration file.")
         self.sigConfigFileChanged.emit(cfg_file)
 
     def getCFGFilePath(self):

tomwer/gui/utils/lineselector/lineselection.py

@@ -0,0 +1,76 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "25/09/2017"
+
+import re
+import numpy
+
+SELECTION_PATTERN = re.compile(r"\d?[:]?\d?")
+
+
+def selectionIsValid(selection):
+    """
+    Return true if the given selection as a string is valid
+
+    :return: bool
+    """
+    assert type(selection) is str
+    _selection = selection.replace(" ", "")
+    selections = _selection.split(";")
+    for sel in selections:
+        if not re.match(SELECTION_PATTERN, sel):
+            return False
+    return True
+
+
+def getSelection(projections, selection):
+    """
+
+    :param str selection:
+    :return numpy.ndarray:
+    """
+
+    def evalSelection(projections, sel):
+        assert type(projections) is numpy.ndarray
+        return eval("projections[" + sel + "]")
+
+    assert type(selection) is str
+    if selection == "":
+        return projections
+    _selection = selection.replace(" ", "")
+    selections = _selection.split(";")
+    if len(selections) == 1:
+        return evalSelection(projections, selection)
+    else:
+        res = None
+        for iSel, sel in enumerate(range(len(selections))):
+            if iSel == 0:
+                res = evalSelection(projections, selections[iSel])
+            else:
+                res = numpy.append(res, evalSelection(projections, selections[iSel]))
+        return res

tomwer/gui/utils/lineselector/lineselector.py

@@ -29,12 +29,13 @@ __license__ = "MIT"
 __date__ = "15/09/2017"
 
 import logging
-from silx.gui import qt
-from silx.gui.plot import PlotWidget
-from typing import Union, Optional
-from collections.abc import Iterable
 from collections import OrderedDict
+from collections.abc import Iterable
+from typing import Optional, Union
+
 import numpy
+from silx.gui import qt
+from silx.gui.plot import PlotWidget
 
 logger = logging.getLogger(__name__)
 
@@ -76,10 +77,7 @@ class QSliceSelectorDialog(qt.QDialog):
         """
         if self.nRequiredSlice() is not None and len(selection) > self.nRequiredSlice():
             raise ValueError(
-                "you provide a selection of {} elements when "
-                "the user should select {}".format(
-                    len(selection), self._n_required_slice
-                )
+                f"you provide a selection of {len(selection)} elements when the user should select {self._n_required_slice}"
             )
         if type(selection) is str:
             selection = selection.replace("(", "")

tomwer/gui/utils/qt_utils.py

@@ -1,4 +1,5 @@
 from contextlib import contextmanager
+
 from silx.gui import qt
 
 

tomwer/gui/utils/scandescription.py

@@ -28,7 +28,9 @@ __date__ = "04/02/2020"
 
 
 from typing import Optional
+
 from silx.gui import qt
+
 from tomwer.core.scan.scanbase import TomwerScanBase
 
 

tomwer/gui/utils/splashscreen.py

@@ -32,8 +32,8 @@ try:
     from silx.gui import qt
 except ImportError:
     raise ImportError("Can't found silx modules")
-from tomwer.gui import icons
 import tomwer.version
+from tomwer.gui import icons
 
 
 def getMainSplashScreen():

tomwer/gui/utils/unitsystem.py

@@ -32,10 +32,12 @@ __license__ = "MIT"
 __date__ = "21/09/2018"
 
 
+import logging
+
 from silx.gui import qt
 from tomoscan.unitsystem import metricsystem
+
 from tomwer.core.utils.char import MU_CHAR
-import logging
 
 _logger = logging.getLogger(__name__)
 

tomwer/gui/utils/vignettes.py

@@ -35,15 +35,15 @@ __license__ = "MIT"
 __date__ = "26/02/2021"
 
 
+import logging
+from typing import Iterable, Union
+
+import numpy
 from silx.gui import qt
-from silx.io.url import DataUrl
 from silx.gui.plot import PlotWindow
-from typing import Union
-from typing import Iterable
-from tomoscan.esrf.scan.utils import get_data
 from silx.gui.plot.utils.axis import SyncAxes
-import numpy
-import logging
+from silx.io.url import DataUrl
+from tomoscan.esrf.scan.utils import get_data
 
 from tomwer.core.process.reconstruction.scores.scores import ComputedScore
 
@@ -380,13 +380,13 @@ class ValueLabel(qt.QWidget):
             str_value = value_format.format(value)
         else:
             str_value = str(value)
-        txt = "{}: {}".format(value_name, str_value)
+        txt = f"{value_name}: {str_value}"
         self._valueLabel = qt.QLabel(txt, self)
         self.layout().addWidget(self._valueLabel)
         if score_format is not None:
             str_score = score_format.format(score)
         else:
             str_score = str(score)
-        txt = "({}: {})".format(score_name, str_score)
+        txt = f"({score_name}: {str_score})"
         self._scoreLabel = qt.QLabel(txt, self)
         self.layout().addWidget(self._scoreLabel)

tomwer/gui/utils/waiterthread.py

@@ -33,9 +33,10 @@ __license__ = "MIT"
 __date__ = "09/02/2017"
 
 
-from silx.gui import qt
 import time
 
+from silx.gui import qt
+
 
 class QWaiterThread(qt.QThread):
     """simple thread wich wait for waitingTime to be finished"""