tomwer 1.3.0.dev2__py3-none-any.whl → 1.3.0rc10__py3-none-any.whl

tomwer/io/utils/h5pyutils.py

@@ -35,7 +35,7 @@ import contextlib
 
 import h5py
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File
+from tomoscan.io import HDF5File, get_swmr_mode
 
 
 class _BaseReader(contextlib.AbstractContextManager):
@@ -60,7 +60,9 @@ class EntryReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(
+            filename=self._url.file_path(), mode="r", swmr=get_swmr_mode()
+        )
         entry = self._file_handler[self._url.data_path()]
         if not isinstance(entry, h5py.Group):
             raise ValueError("Data path should point to a bliss node (h5py.Group)")
@@ -71,7 +73,9 @@ class DatasetReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(
+            filename=self._url.file_path(), mode="r", swmr=get_swmr_mode()
+        )
         entry = self._file_handler[self._url.data_path()]
         if not isinstance(entry, h5py.Dataset):
             raise ValueError("Data path should point to a dtaset (h5py.Dataset)")

tomwer/io/utils/utils.py

@@ -39,7 +39,7 @@ 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 tomoscan.io import HDF5File, get_swmr_mode
 from typing import Union
 
 from tomwer.core.utils import ftseriesutils
@@ -201,7 +201,7 @@ def get_linked_files_with_entry(hdf5_file: str, entry: str) -> set:
             if item in treated_items:
                 continue
             dirname = os.path.dirname(abs_file_path)
-            with HDF5File(abs_file_path, mode="r") as h5f:
+            with HDF5File(abs_file_path, mode="r", swmr=get_swmr_mode()) as h5f:
                 node = h5f.get(data_path, getlink=True)
                 if isinstance(node, h5py.ExternalLink):
                     ext_file_path = node.filename
@@ -252,7 +252,7 @@ def get_linked_files_with_vds(hdf5_file: str, dataset_path: str) -> set:
             if item in treated_items:
                 continue
             dirname = os.path.dirname(abs_file_path)
-            with HDF5File(abs_file_path, mode="r") as h5f:
+            with HDF5File(abs_file_path, mode="r", swmr=get_swmr_mode()) as h5f:
                 dataset = h5f[dataset_path]
                 if dataset.is_virtual:
                     for vs_info in dataset.virtual_sources():

tomwer/resources/gui/icons/parameters.svg

@@ -14,7 +14,7 @@
    id="svg2985"
    version="1.1"
    inkscape:version="0.48.5 r10040"
-   sodipodi:docname="lamino_parameters.svg"
+   sodipodi:docname="parameters.svg"
    inkscape:export-filename="/nobackup/linazimov/payno/dev/esrf/ID06/id06workflow/resources/gui/icons/input.png"
    inkscape:export-xdpi="200"
    inkscape:export-ydpi="200">

tomwer/resources/gui/illustrations/no_rot.svg

@@ -14,7 +14,7 @@
    height="160"
    version="1.1"
    inkscape:version="0.48.5 r10040"
-   sodipodi:docname="lamino_beta_angle.svg">
+   sodipodi:docname="no_rot.svg">
   <sodipodi:namedview
      pagecolor="#ffffff"
      bordercolor="#666666"

tomwer/synctools/stacks/edit/darkflatpatch.py

@@ -142,18 +142,23 @@ class _DarkFlatPatchProcessingThread(ProcessingThread, SuperviseProcess):
         for key in keys:
             if isinstance(configuration_to_dump[key], DataUrl):
                 configuration_to_dump[key] = configuration_to_dump[key].path()
-        try:
-            darkflatpatch.DarkFlatPatchTask._register_process(
-                process_file=self._scan.process_file,
-                entry=entry,
-                configuration=configuration_to_dump,
-                results={},
-                process=darkflatpatch.DarkFlatPatchTask,
-                process_index=index,
-                overwrite=True,
-            )
-        except Exception as e:
-            _logger.warning(f"Fail to register DarkFlatPatch process. Reason is {e}")
+
+        with self._scan.acquire_process_file_lock():
+
+            try:
+                darkflatpatch.DarkFlatPatchTask._register_process(
+                    process_file=self._scan.process_file,
+                    entry=entry,
+                    configuration=configuration_to_dump,
+                    results={},
+                    process=darkflatpatch.DarkFlatPatchTask,
+                    process_index=index,
+                    overwrite=True,
+                )
+            except Exception as e:
+                _logger.warning(
+                    f"Fail to register DarkFlatPatch process. Reason is {e}"
+                )
         info = f"Dark-flat patched for {self._scan}."
         _logger.processSucceed(info)
         ProcessManager().notify_dataset_state(

tomwer/tests/test_scripts.py

@@ -79,9 +79,6 @@ class TestScriptsHelp(unittest.TestCase):
             "intensity-normalization", "tomwer.app.intensitynormalization"
         )
 
-    def testLamino(self):
-        self.executeAppHelp("lamino", "tomwer.app.lamino")
-
     def testMulticor(self):
         self.executeAppHelp("multicor", "tomwer.app.multicor")
 

tomwer/third_part/WaitingOverlay.py

@@ -0,0 +1,110 @@
+from typing import Optional
+from silx.gui.widgets.WaitingPushButton import WaitingPushButton
+from silx.gui import qt
+from silx.gui.qt import inspect as qt_inspect
+from silx.gui.plot import PlotWidget
+
+
+class WaitingOverlay(qt.QWidget):
+    """Widget overlaying another widget with a processing wheel icon.
+
+    :param parent: widget on top of which to display the "processing/waiting wheel"
+    """
+
+    def __init__(self, parent: qt.QWidget) -> None:
+        super().__init__(parent)
+        self.setContentsMargins(0, 0, 0, 0)
+
+        self._waitingButton = WaitingPushButton(self)
+        self._waitingButton.setDown(True)
+        self._waitingButton.setWaiting(True)
+        self._waitingButton.setStyleSheet(
+            "QPushButton { background-color: rgba(150, 150, 150, 40); border: 0px; border-radius: 10px; }"
+        )
+        self._registerParent(parent)
+
+    def text(self) -> str:
+        """Returns displayed text"""
+        return self._waitingButton.text()
+
+    def setText(self, text: str):
+        """Set displayed text"""
+        self._waitingButton.setText(text)
+        self._resize()
+
+    def _listenedWidget(self, parent: qt.QWidget) -> qt.QWidget:
+        """Returns widget to register event filter to according to parent"""
+        if isinstance(parent, PlotWidget):
+            return parent.getWidgetHandle()
+        return parent
+
+    def _backendChanged(self):
+        self._listenedWidget(self.parent()).installEventFilter(self)
+        self._resizeLater()
+
+    def _registerParent(self, parent: Optional[qt.QWidget]):
+        if parent is None:
+            return
+        self._listenedWidget(parent).installEventFilter(self)
+        if isinstance(parent, PlotWidget):
+            parent.sigBackendChanged.connect(self._backendChanged)
+        self._resize()
+
+    def _unregisterParent(self, parent: Optional[qt.QWidget]):
+        if parent is None:
+            return
+        if isinstance(parent, PlotWidget):
+            parent.sigBackendChanged.disconnect(self._backendChanged)
+        self._listenedWidget(parent).removeEventFilter(self)
+
+    def setParent(self, parent: qt.QWidget):
+        self._unregisterParent(self.parent())
+        super().setParent(parent)
+        self._registerParent(parent)
+
+    def showEvent(self, event: qt.QShowEvent):
+        super().showEvent(event)
+        self._waitingButton.setVisible(True)
+
+    def hideEvent(self, event: qt.QHideEvent):
+        super().hideEvent(event)
+        self._waitingButton.setVisible(False)
+
+    def _resize(self):
+        if not qt_inspect.isValid(self):
+            return  # For _resizeLater in case the widget has been deleted
+
+        parent = self.parent()
+        if parent is None:
+            return
+
+        size = self._waitingButton.sizeHint()
+        if isinstance(parent, PlotWidget):
+            offset = parent.getWidgetHandle().mapTo(parent, qt.QPoint(0, 0))
+            left, top, width, height = parent.getPlotBoundsInPixels()
+            rect = qt.QRect(
+                qt.QPoint(
+                    int(offset.x() + left + width / 2 - size.width() / 2),
+                    int(offset.y() + top + height / 2 - size.height() / 2),
+                ),
+                size,
+            )
+        else:
+            position = parent.size()
+            position = (position - size) / 2
+            rect = qt.QRect(qt.QPoint(position.width(), position.height()), size)
+        self.setGeometry(rect)
+        self.raise_()
+
+    def _resizeLater(self):
+        qt.QTimer.singleShot(0, self._resize)
+
+    def eventFilter(self, watched: qt.QWidget, event: qt.QEvent):
+        if event.type() == qt.QEvent.Resize:
+            self._resize()
+            self._resizeLater()  # Defer resize for the receiver to have handled it
+        return super().eventFilter(watched, event)
+
+    # expose Waiting push button API
+    def setIconSize(self, size):
+        self._waitingButton.setIconSize(size)

tomwer/version.py

@@ -78,8 +78,8 @@ RELEASE_LEVEL_VALUE = {
 MAJOR = 1
 MINOR = 3
 MICRO = 0
-RELEV = "dev"  # <16
-SERIAL = 2  # <16
+RELEV = "rc"  # <16
+SERIAL = 10  # <16
 
 date = __date__
 

{tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.0.dev2
+Version: 1.3.0rc10
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -24,16 +24,16 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: setuptools
 Requires-Dist: psutil
-Requires-Dist: silx (<2.0,>=1.0)
-Requires-Dist: tomoscan (>=2.0.0a11)
-Requires-Dist: nxtomo (>=1.0.4)
-Requires-Dist: nxtomomill (>=1.0dev)
-Requires-Dist: processview (>=1.3)
-Requires-Dist: ewoks (>=0.1.1)
-Requires-Dist: sluurp (>=0.3.3)
+Requires-Dist: silx[full] >=2.0
+Requires-Dist: tomoscan >=2.0.0a11
+Requires-Dist: nxtomo >=1.2.3rc1
+Requires-Dist: nxtomomill >=1.0dev
+Requires-Dist: processview >=1.3
+Requires-Dist: ewoks >=0.1.1
+Requires-Dist: sluurp >=0.3.3
 Requires-Dist: packaging
 Requires-Dist: flufl-lock
-Requires-Dist: pyunitsystem (>=1.1.0)
+Requires-Dist: pyunitsystem >=1.1.0
 Provides-Extra: _dev_spec
 Requires-Dist: black ; extra == '_dev_spec'
 Requires-Dist: flake8 ; extra == '_dev_spec'
@@ -42,11 +42,11 @@ Requires-Dist: pyopencl ; extra == '_dev_spec'
 Provides-Extra: _full_base
 Requires-Dist: orange-canvas-core ; extra == '_full_base'
 Requires-Dist: orange-widget-base ; extra == '_full_base'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == '_full_base'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == '_full_base'
 Requires-Dist: rsyncmanager ; extra == '_full_base'
 Requires-Dist: graypy ; extra == '_full_base'
 Requires-Dist: fabio ; extra == '_full_base'
-Requires-Dist: h5py (>=3) ; extra == '_full_base'
+Requires-Dist: h5py >=3 ; extra == '_full_base'
 Requires-Dist: lxml ; extra == '_full_base'
 Requires-Dist: werkzeug ; extra == '_full_base'
 Requires-Dist: json-rpc ; extra == '_full_base'
@@ -60,11 +60,11 @@ Requires-Dist: pyicat-plus ; extra == '_full_base'
 Provides-Extra: dev
 Requires-Dist: orange-canvas-core ; extra == 'dev'
 Requires-Dist: orange-widget-base ; extra == 'dev'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'dev'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'dev'
 Requires-Dist: rsyncmanager ; extra == 'dev'
 Requires-Dist: graypy ; extra == 'dev'
 Requires-Dist: fabio ; extra == 'dev'
-Requires-Dist: h5py (>=3) ; extra == 'dev'
+Requires-Dist: h5py >=3 ; extra == 'dev'
 Requires-Dist: lxml ; extra == 'dev'
 Requires-Dist: werkzeug ; extra == 'dev'
 Requires-Dist: json-rpc ; extra == 'dev'
@@ -75,7 +75,7 @@ Requires-Dist: resource ; extra == 'dev'
 Requires-Dist: tifffile ; extra == 'dev'
 Requires-Dist: hdf5plugin ; extra == 'dev'
 Requires-Dist: pyicat-plus ; extra == 'dev'
-Requires-Dist: nabu[full] (>=2023.3.0dev) ; extra == 'dev'
+Requires-Dist: nabu[full] >=2023.3.1dev ; extra == 'dev'
 Requires-Dist: pycuda ; extra == 'dev'
 Requires-Dist: scikit-cuda ; extra == 'dev'
 Requires-Dist: black ; extra == 'dev'
@@ -85,11 +85,11 @@ Requires-Dist: pyopencl ; extra == 'dev'
 Provides-Extra: dev_no_cuda
 Requires-Dist: orange-canvas-core ; extra == 'dev_no_cuda'
 Requires-Dist: orange-widget-base ; extra == 'dev_no_cuda'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'dev_no_cuda'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'dev_no_cuda'
 Requires-Dist: rsyncmanager ; extra == 'dev_no_cuda'
 Requires-Dist: graypy ; extra == 'dev_no_cuda'
 Requires-Dist: fabio ; extra == 'dev_no_cuda'
-Requires-Dist: h5py (>=3) ; extra == 'dev_no_cuda'
+Requires-Dist: h5py >=3 ; extra == 'dev_no_cuda'
 Requires-Dist: lxml ; extra == 'dev_no_cuda'
 Requires-Dist: werkzeug ; extra == 'dev_no_cuda'
 Requires-Dist: json-rpc ; extra == 'dev_no_cuda'
@@ -100,7 +100,7 @@ Requires-Dist: resource ; extra == 'dev_no_cuda'
 Requires-Dist: tifffile ; extra == 'dev_no_cuda'
 Requires-Dist: hdf5plugin ; extra == 'dev_no_cuda'
 Requires-Dist: pyicat-plus ; extra == 'dev_no_cuda'
-Requires-Dist: nabu (>=2023.3.0dev) ; extra == 'dev_no_cuda'
+Requires-Dist: nabu >=2023.3.1dev ; extra == 'dev_no_cuda'
 Requires-Dist: black ; extra == 'dev_no_cuda'
 Requires-Dist: flake8 ; extra == 'dev_no_cuda'
 Requires-Dist: timeout-decorator ; extra == 'dev_no_cuda'
@@ -108,11 +108,11 @@ Requires-Dist: pyopencl ; extra == 'dev_no_cuda'
 Provides-Extra: doc
 Requires-Dist: orange-canvas-core ; extra == 'doc'
 Requires-Dist: orange-widget-base ; extra == 'doc'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'doc'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'doc'
 Requires-Dist: rsyncmanager ; extra == 'doc'
 Requires-Dist: graypy ; extra == 'doc'
 Requires-Dist: fabio ; extra == 'doc'
-Requires-Dist: h5py (>=3) ; extra == 'doc'
+Requires-Dist: h5py >=3 ; extra == 'doc'
 Requires-Dist: lxml ; extra == 'doc'
 Requires-Dist: werkzeug ; extra == 'doc'
 Requires-Dist: json-rpc ; extra == 'doc'
@@ -123,21 +123,22 @@ Requires-Dist: resource ; extra == 'doc'
 Requires-Dist: tifffile ; extra == 'doc'
 Requires-Dist: hdf5plugin ; extra == 'doc'
 Requires-Dist: pyicat-plus ; extra == 'doc'
-Requires-Dist: nabu (>=2023.3.0dev) ; extra == 'doc'
-Requires-Dist: Sphinx (>=4.0.0) ; extra == 'doc'
+Requires-Dist: nabu >=2023.3.1dev ; extra == 'doc'
+Requires-Dist: Sphinx >=4.0.0 ; extra == 'doc'
 Requires-Dist: nbsphinx ; extra == 'doc'
 Requires-Dist: pandoc ; extra == 'doc'
 Requires-Dist: jupyterlab ; extra == 'doc'
 Requires-Dist: pydata-sphinx-theme ; extra == 'doc'
 Requires-Dist: sphinx-design ; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints ; extra == 'doc'
 Provides-Extra: full
 Requires-Dist: orange-canvas-core ; extra == 'full'
 Requires-Dist: orange-widget-base ; extra == 'full'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'full'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'full'
 Requires-Dist: rsyncmanager ; extra == 'full'
 Requires-Dist: graypy ; extra == 'full'
 Requires-Dist: fabio ; extra == 'full'
-Requires-Dist: h5py (>=3) ; extra == 'full'
+Requires-Dist: h5py >=3 ; extra == 'full'
 Requires-Dist: lxml ; extra == 'full'
 Requires-Dist: werkzeug ; extra == 'full'
 Requires-Dist: json-rpc ; extra == 'full'
@@ -148,17 +149,17 @@ Requires-Dist: resource ; extra == 'full'
 Requires-Dist: tifffile ; extra == 'full'
 Requires-Dist: hdf5plugin ; extra == 'full'
 Requires-Dist: pyicat-plus ; extra == 'full'
-Requires-Dist: nabu[full] (>=2023.3.0dev) ; extra == 'full'
+Requires-Dist: nabu[full] >=2023.3.1dev ; extra == 'full'
 Requires-Dist: pycuda ; extra == 'full'
 Requires-Dist: scikit-cuda ; extra == 'full'
 Provides-Extra: full_no_cuda
 Requires-Dist: orange-canvas-core ; extra == 'full_no_cuda'
 Requires-Dist: orange-widget-base ; extra == 'full_no_cuda'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'full_no_cuda'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'full_no_cuda'
 Requires-Dist: rsyncmanager ; extra == 'full_no_cuda'
 Requires-Dist: graypy ; extra == 'full_no_cuda'
 Requires-Dist: fabio ; extra == 'full_no_cuda'
-Requires-Dist: h5py (>=3) ; extra == 'full_no_cuda'
+Requires-Dist: h5py >=3 ; extra == 'full_no_cuda'
 Requires-Dist: lxml ; extra == 'full_no_cuda'
 Requires-Dist: werkzeug ; extra == 'full_no_cuda'
 Requires-Dist: json-rpc ; extra == 'full_no_cuda'
@@ -169,15 +170,15 @@ Requires-Dist: resource ; extra == 'full_no_cuda'
 Requires-Dist: tifffile ; extra == 'full_no_cuda'
 Requires-Dist: hdf5plugin ; extra == 'full_no_cuda'
 Requires-Dist: pyicat-plus ; extra == 'full_no_cuda'
-Requires-Dist: nabu (>=2023.3.0dev) ; extra == 'full_no_cuda'
+Requires-Dist: nabu >=2023.3.1dev ; extra == 'full_no_cuda'
 Provides-Extra: full_no_nabu
 Requires-Dist: orange-canvas-core ; extra == 'full_no_nabu'
 Requires-Dist: orange-widget-base ; extra == 'full_no_nabu'
-Requires-Dist: ewoks[orange] (>=0.1.1) ; extra == 'full_no_nabu'
+Requires-Dist: ewoks[orange] >=0.1.1 ; extra == 'full_no_nabu'
 Requires-Dist: rsyncmanager ; extra == 'full_no_nabu'
 Requires-Dist: graypy ; extra == 'full_no_nabu'
 Requires-Dist: fabio ; extra == 'full_no_nabu'
-Requires-Dist: h5py (>=3) ; extra == 'full_no_nabu'
+Requires-Dist: h5py >=3 ; extra == 'full_no_nabu'
 Requires-Dist: lxml ; extra == 'full_no_nabu'
 Requires-Dist: werkzeug ; extra == 'full_no_nabu'
 Requires-Dist: json-rpc ; extra == 'full_no_nabu'
@@ -190,10 +191,10 @@ Requires-Dist: hdf5plugin ; extra == 'full_no_nabu'
 Requires-Dist: pyicat-plus ; extra == 'full_no_nabu'
 Provides-Extra: setup_requires
 Requires-Dist: setuptools ; extra == 'setup_requires'
-Requires-Dist: numpy (>=1.12) ; extra == 'setup_requires'
+Requires-Dist: numpy >=1.12 ; extra == 'setup_requires'
 Provides-Extra: test
 Requires-Dist: pytest-asyncio ; extra == 'test'
-Requires-Dist: tomoscan[test] (>=2.0.0a11) ; extra == 'test'
+Requires-Dist: tomoscan[test] >=2.0.2rc17 ; extra == 'test'
 
 tomwer
 ======