tomwer 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

tomwer/{web/__init__.py → gui/control/serie/seriewaiter.py}

@@ -1,6 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
-# Copyright (C) 2016 European Synchrotron Radiation Facility
+#
+# Copyright (c) 2016-2017 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
@@ -20,11 +21,8 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 #
-#############################################################################*/
-"""Module containing process relative to the web (like classes used to link
-with graylog)
-"""
+# ###########################################################################*/
 
-__authors__ = ["H.Payno"]
+__authors__ = ["H. Payno"]
 __license__ = "MIT"
-__date__ = "15/05/2017"
+__date__ = "12/01/2022"

tomwer/gui/control/singletomoobj.py

@@ -23,7 +23,6 @@ _logger = logging.getLogger(__name__)
 
 
 class SingleTomoObj(qt.QWidget):
-
     sigTomoObjChanged = qt.Signal(str)
     """signal emit when the tomo object changed. Parameter is the identifier"""
 
@@ -51,7 +50,7 @@ class SingleTomoObj(qt.QWidget):
     def getTomoObjIdentifier(self) -> str:
         return self._tomoObjIdentifierLineQLE.text()
 
-    def _selectObject(self, *args, **kwargs):
+    def _selectObject(self, *args, **kwargs):  # pragma: no cover
         dialog = QDataDialog(self, multiSelection=True)
         dialog.setNameFilters(
             [
@@ -111,7 +110,7 @@ class SingleTomoObj(qt.QWidget):
             return ScanFactory.create_scan_objects(path)
         except:  # noqa E722
             try:
-                return guess_volumes(
+                volumes = guess_volumes(
                     path,
                     scheme_to_vol={
                         EDFVolumeIdentifier.scheme: EDFVolume,
@@ -124,7 +123,19 @@ class SingleTomoObj(qt.QWidget):
                 )
             except:  # noqa E722
                 pass
-        return None
+                return None
+            else:
+                # filter potential 'nabu histogram'
+                if volumes is not None:
+
+                    def is_not_histogram(vol_identifier):
+                        return not (
+                            hasattr(vol_identifier, "data_path")
+                            and vol_identifier.data_path.endswith("histogram")
+                        )
+
+                    volumes = tuple(filter(is_not_histogram, volumes))
+                return volumes
 
 
 class _TomoObjQLE(QLFileSystem):

tomwer/gui/control/test/test_datalist.py

@@ -29,7 +29,7 @@ __date__ = "05/11/2018"
 
 from tomwer.gui.control.datalist import GenericScanListDialog
 from tomwer.gui.control.datalist import VolumeList
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
 from tomwer.core.utils.scanutils import MockEDF
 from silx.gui import qt

tomwer/gui/control/test/test_datalistener.py

@@ -30,7 +30,7 @@ __date__ = "18/03/2020"
 
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from tomwer.gui.control.datalistener import ConfigurationWidget
 from silx.gui.utils.testutils import SignalListener
 import pytest

tomwer/gui/control/test/test_inputwidget.py

@@ -28,7 +28,7 @@ __date__ = "16/06/2021"
 
 
 from tomwer.gui.utils import inputwidget
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
 from silx.gui import qt
 import numpy

tomwer/gui/control/test/test_process_manager.py

@@ -28,11 +28,10 @@ __license__ = "MIT"
 __date__ = "09/11/2020"
 
 
-import unittest
 import pytest
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from tomwer.gui.control.datalistener import ConfigurationWidget
 from silx.gui.utils.testutils import SignalListener
 
@@ -64,14 +63,3 @@ class TestProcessManager(TestCaseQt):
         self.assertEqual(
             self._configWidget.getConfiguration(), {"host": "toto", "port": 0}
         )
-
-
-def suite():
-    test_suite = unittest.TestSuite()
-    for ui in (TestProcessManager,):
-        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
-    return test_suite
-
-
-if __name__ == "__main__":
-    unittest.main(defaultTest="suite")

tomwer/gui/control/test/test_scanselector.py

@@ -27,7 +27,7 @@ __license__ = "MIT"
 __date__ = "22/01/2017"
 
 
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
 from tomwer.gui.control.scanselectorwidget import ScanSelectorWidget
 from tomwer.core.utils.scanutils import MockEDF

tomwer/gui/control/test/test_scanvalidator.py

@@ -41,7 +41,7 @@ from tomwer.core.utils.scanutils import MockEDF
 from tomwer.core.process.control.scanvalidator import ScanValidatorP
 from tomwer.gui.utils.waiterthread import QWaiterThread
 from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 
 logging.disable(logging.INFO)
 

tomwer/gui/control/test/test_single_tomo_obj.py

@@ -22,7 +22,7 @@ class TestSingletomoObj(TestCaseQt):
         self.volume = HDF5Volume(
             file_path=self._volume_file_path,
             data_path="my_volume",
-            data=numpy.linspace(0, 200, 200).reshape(2, 10, 10),
+            data=numpy.linspace(start=0, stop=200, num=200).reshape((2, 10, 10)),
         )
         self.volume.save()
 

tomwer/gui/control/test/test_volume_dialog.py

@@ -34,7 +34,7 @@ import shutil
 import tempfile
 from silx.gui.utils.testutils import TestCaseQt
 from silx.gui import qt
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from tomwer.gui.qfolderdialog import QVolumeDialog
 from tomoscan.esrf.volume.edfvolume import EDFVolume
 from tomoscan.esrf.volume.hdf5volume import HDF5Volume
@@ -67,7 +67,9 @@ class TestVolumeDialog(TestCaseQt):
         volume = HDF5Volume(
             file_path=file_path,
             data_path="entry",
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
         )
         volume.save()
         self._dialog.show()
@@ -93,7 +95,9 @@ class TestVolumeDialog(TestCaseQt):
         volume = HDF5Volume(
             file_path=file_path,
             data_path="entry",
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
         )
         volume.save()
 
@@ -115,7 +119,9 @@ class TestVolumeDialog(TestCaseQt):
         self._dialog.setFullAuto(True)
         volume = EDFVolume(
             folder=self.tmp_dir,
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
         )
         volume.save()
         self._dialog.show()
@@ -140,7 +146,9 @@ class TestVolumeDialog(TestCaseQt):
         self._dialog.setFullAuto(False)
         volume = EDFVolume(
             folder=self.tmp_dir,
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
             volume_basename="test",
         )
         volume.save()
@@ -168,7 +176,9 @@ class TestVolumeDialog(TestCaseQt):
         volume = HDF5Volume(
             file_path=file_path,
             data_path="entry",
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
         )
         volume.save()
         self._dialog.setVolumeUrl(volume.get_identifier().to_str())
@@ -187,7 +197,9 @@ class TestVolumeDialog(TestCaseQt):
         """
         volume = EDFVolume(
             folder=self.tmp_dir,
-            data=numpy.linspace(1, 10, 300, dtype=numpy.uint8).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=10, num=300, dtype=numpy.uint8).reshape(
+                (3, 10, 10)
+            ),
             volume_basename="test",
         )
         volume.save()

tomwer/gui/control/test/test_volumeselector.py

@@ -28,7 +28,7 @@ __date__ = "22/01/2017"
 
 
 import os
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
 from tomwer.gui.control.volumeselectorwidget import VolumeSelectorWidget
@@ -52,20 +52,20 @@ class TestVolumeSelector(TestCaseQt):
         self.volume_1 = HDF5Volume(
             file_path=os.path.join(self.folder, "my_volume.hdf5"),
             data_path="entry0000",
-            data=numpy.linspace(1, 100, 300).reshape(3, 10, 10),
+            data=numpy.linspace(start=1, stop=100, num=300).reshape((3, 10, 10)),
         )
         self.volume_1.save()
 
         self.volume_2 = HDF5Volume(
             file_path=os.path.join(self.folder, "my_volume.hdf5"),
             data_path="entry0001",
-            data=numpy.linspace(1, 100, 400).reshape(4, 10, 10),
+            data=numpy.linspace(start=1, stop=100, num=400).reshape((4, 10, 10)),
         )
         self.volume_2.save()
 
         self.volume_3 = EDFVolume(
             folder=os.path.join(self.folder, "vol"),
-            data=numpy.linspace(1, 100, 500).reshape(5, 10, 10),
+            data=numpy.linspace(start=1, stop=100, num=500).reshape((5, 10, 10)),
         )
         self.volume_3.save()
 

tomwer/gui/debugtools/datasetgenerator.py

@@ -37,7 +37,6 @@ from tomwer.core.scan.blissscan import BlissScan
 
 
 class DatasetGeneratorDialog(qt.QDialog):
-
     sigGenerationStarted = qt.Signal()
     """signal emitted when the generation is started"""
 
@@ -183,7 +182,7 @@ class DatasetGeneratorConfig(qt.QWidget):
     def _signalUpdated(self, *args, **kwargs):
         self.sigConfigChanged.emit()
 
-    def _selectRootFolder(self):
+    def _selectRootFolder(self):  # pragma: no cover
         defaultDirectory = self._outputQLE.text()
         dialog = qt.QFileDialog(self, directory=defaultDirectory)
         dialog.setFileMode(qt.QFileDialog.DirectoryOnly)
@@ -278,10 +277,3 @@ class DatasetGeneratorConfig(qt.QWidget):
         if "flat_at_beginning" in config:
             self.setFlatNeededAtBeginning(config["flat_at_beginning"])
         self.blockSignals(old)
-
-
-if __name__ == "__main__":
-    app = qt.QApplication([])
-    dialog = DatasetGeneratorDialog(parent=None)
-    dialog.show()
-    app.exec_()

tomwer/gui/edit/dkrfpatch.py

@@ -31,7 +31,7 @@ __date__ = "30/10/2020"
 import h5py
 from silx.gui import qt
 from silx.io.utils import h5py_read_dataset
-from tomoscan.esrf.hdf5scan import ImageKey
+from tomoscan.esrf.scan.hdf5scan import ImageKey
 from silx.io.url import DataUrl
 from tomoscan.io import HDF5File
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
@@ -46,7 +46,6 @@ _logger = logging.getLogger(__name__)
 
 
 class _DarkOrFlatUrl(qt.QWidget):
-
     editingFinished = qt.Signal()
     """Signal emit when the url changes"""
 
@@ -242,7 +241,7 @@ class _DarkOrFlatUrl(qt.QWidget):
                 scheme="silx",
             )
         except Exception as e:
-            _logger.warning("Fail to create url. Reason is", str(e))
+            _logger.warning(f"Fail to create url. Reason is {e}")
             return None
         else:
             return url

tomwer/gui/edit/imagekeyeditor.py

@@ -32,7 +32,7 @@ from silx.gui import qt
 from tomwer.core.process.edit.imagekeyeditor import IMAGE_KEYS
 from typing import Union
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomoscan.esrf.hdf5scan import ImageKey as _ImageKey
+from tomoscan.esrf.scan.hdf5scan import ImageKey as _ImageKey
 import weakref
 import functools
 from collections.abc import Iterable
@@ -154,7 +154,6 @@ class ImageKeyWindow(qt.QMainWindow):
 
 
 class _ImageKeyEditor(qt.QDialog):
-
     sigApply = qt.Signal()
     """Signal emitted when the user request to apply the current modifications
     """
@@ -172,7 +171,7 @@ class _ImageKeyEditor(qt.QDialog):
         # mode selection
         self.layout().addWidget(qt.QLabel("selection mode"), 1, 0, 1, 1)
         self._selectionModeCB = qt.QComboBox(self)
-        for mode in ("slice", "list"):
+        for mode in ("range", "list"):
             self._selectionModeCB.addItem(mode)
         self._selectionModeCB.setCurrentIndex(self._selectionModeCB.findText("list"))
         self.layout().addWidget(self._selectionModeCB, 1, 1, 1, 1)
@@ -225,7 +224,7 @@ class _ImageKeyEditor(qt.QDialog):
     def getSelectionMode(self) -> str:
         """
 
-        :return: frame indexes selection mode. Can be 'slice' or 'list'
+        :return: frame indexes selection mode. Can be 'range' or 'list'
         """
         return self._selectionModeCB.currentText()
 
@@ -235,7 +234,7 @@ class _ImageKeyEditor(qt.QDialog):
         :return: list of indexes to be modified
         :rtype: list
         """
-        if self.getSelectionMode() == "slice":
+        if self.getSelectionMode() == "range":
             return self._selectionWidget.getSlice()
         elif self.getSelectionMode() == "list":
             return self._selectionWidget.getList()
@@ -322,7 +321,7 @@ class _ListSelection(qt.QWidget):
     def _selectFrames(self):
         if self._scan is None or self._scan() is None:
             _logger.warning(
-                "No scan set or has been moved. Unable to select " "slices from it."
+                "No scan set or has been moved. Unable to select slices from it."
             )
             return
         scan = self._scan()
@@ -376,11 +375,14 @@ class _EditionSelection(qt.QWidget):
     def setSelectionMode(self, mode: str) -> None:
         """
 
-        :param str mode: define indexes selection mode. Can be 'slice' or
+        :param str mode: define indexes selection mode. Can be 'range' or
                          'list'
         """
-        assert mode in ("slice", "list")
-        self._sliceSelection.setVisible(mode == "slice")
+        if mode == "slice":
+            # for backward compatibility (user can have .ows with old name)
+            mode = "range"
+        assert mode in ("range", "list")
+        self._sliceSelection.setVisible(mode == "range")
         self._listSelection.setVisible(mode == "list")
 
     def getList(self) -> list:
@@ -446,7 +448,7 @@ class _ImageKeyList(qt.QTableWidget):
         """
         Update the QTableWidget for the provided frames
 
-        :param Iterable frames: Iterable of tomoscan.esrf.HDF5TomoScan.Frame
+        :param Iterable frames: Iterable of tomoscan.esrf.scan.HDF5TomoScan.Frame
         :param dict frames_new_keys: dictionary with frame edited. key is frame
                                      index. Value is the new `image_key` value
         """
@@ -572,7 +574,6 @@ class _ImageKeyList(qt.QTableWidget):
 
 
 class _ImageKeyListFiltered(qt.QWidget):
-
     MODIFIED_IMG_FILTER = "modified"
     ALL_IMG_FILTER = "all"