tomwer 1.3.4__py3-none-any.whl → 1.3.26__py3-none-any.whl

tomwer/gui/visualization/volumeviewer.py

@@ -15,7 +15,6 @@ from tomoscan.esrf.volume.hdf5volume import HDF5Volume
 from tomoscan.factory import Factory
 from tomoscan.identifier import VolumeIdentifier
 from tomoscan.volumebase import VolumeBase
-from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.visualization.reconstructionparameters import ReconstructionParameters
@@ -298,9 +297,16 @@ class VolumeViewer(qt.QMainWindow):
 
         self._close_h5_file()
         if isinstance(volume, HDF5Volume):
-            self._h5_file = HDF5File(
-                filename=volume.data_url.file_path(), mode="r", swmr=get_swmr_mode()
-            )
+            try:
+                self._h5_file = h5py.File(volume.data_url.file_path(), mode="r")
+            except OSError:
+                self._h5_file = h5py.File(
+                    volume.data_url.file_path(),
+                    mode="r",
+                    libver="latest",
+                    swmr=True,
+                )
+
             if volume.data_url.data_path() in self._h5_file:
                 data = self._h5_file[volume.data_url.data_path()]
                 state = "loaded"

tomwer/io/utils/h5pyutils.py

@@ -35,7 +35,7 @@ import contextlib
 
 import h5py
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
 
 
 class _BaseReader(contextlib.AbstractContextManager):
@@ -60,9 +60,7 @@ 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", swmr=get_swmr_mode()
-        )
+        self._file_handler = open_hdf5(filename=self._url.file_path())
         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)")
@@ -73,9 +71,7 @@ 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", swmr=get_swmr_mode()
-        )
+        self._file_handler = open_hdf5(filename=self._url.file_path())
         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

@@ -37,9 +37,9 @@ import os
 import h5py
 import numpy.lib.npyio
 from PIL import Image
+from silx.io.utils import open as open_hdf5
 from tomoscan.esrf import has_glymur
 from tomoscan.esrf.scan.utils import get_data as tomoscan_get_data
-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", swmr=get_swmr_mode()) as h5f:
+            with open_hdf5(abs_file_path) 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", swmr=get_swmr_mode()) as h5f:
+            with open_hdf5(abs_file_path) as h5f:
                 dataset = h5f[dataset_path]
                 if dataset.is_virtual:
                     for vs_info in dataset.virtual_sources():

tomwer/synctools/stacks/reconstruction/castvolume.py

@@ -94,11 +94,26 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
             self.scan_ready(scan=data)
         else:
             self._data_currently_computed = data
-            self._computationThread.init(data=data, configuration=configuration)
-            # need to manage connect before starting it because
-            fct_callback = functools.partial(self._end_threaded_computation, callback)
-            self._computationThread.finished.connect(fct_callback)
-            self._computationThread.start()
+            try:
+                self._computationThread.init(data=data, configuration=configuration)
+            except ValueError as e:
+                # initialization can fail (for example for cast volume is there is no volume or be case this will raise an error)
+                # then we want to keep the thread active
+                self._data_currently_computed = None
+                ProcessManager().notify_dataset_state(
+                    dataset=data, process=self._process_id, state=DatasetState.SKIPPED
+                )
+                _logger.processSkipped(f"thread initialization failed. Error is {e}")
+                if callback is not None:
+                    callback()
+                self.scan_ready(scan=data)
+            else:
+                # need to manage connect before starting it because
+                fct_callback = functools.partial(
+                    self._end_threaded_computation, callback
+                )
+                self._computationThread.finished.connect(fct_callback)
+                self._computationThread.start()
 
     def _end_computation(self, data, future_tomo_obj, callback):
         """

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -30,6 +30,7 @@ import functools
 import logging
 import shutil
 import tempfile
+import os
 
 from processview.core.manager import DatasetState, ProcessManager
 from processview.core.superviseprocess import SuperviseProcess
@@ -132,6 +133,15 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
     def _create_processing_thread(self, process_id=None) -> qt.QThread:
         return _ProcessingThread(process_id=process_id, save_dir=self._save_dir)
 
+    def clear_cache(self):
+        """
+        remove the file used to cache the reduced darks / flats.
+        This can be used in the case it contain unrelevant data. Like frame with another shape...
+        """
+        cache_file = DarkRefsCopy.get_save_file(self._save_dir)
+        if os.path.exists(cache_file):
+            os.remove(cache_file)
+
 
 class _ProcessingThread(ProcessingThread, SuperviseProcess):
     """

tomwer/tests/datasets.py

@@ -1,5 +1,9 @@
 import os
-from tomoscan.test.datasets import GitlabProject
+
+try:
+    from tomoscan.test.datasets import GitlabProject
+except ImportError:
+    from tomoscan.tests.datasets import GitlabProject
 
 TomwerCIDatasets = GitlabProject(
     branch_name="tomwer",

tomwer/utils.py

@@ -81,10 +81,7 @@ class LauncherCommand(_LauncherCommand):
     """Description of a command"""
 
     def get_module(self):
-        """Returns the python module to execute. If any.
-
-        :rtype: module
-        """
+        """Returns the python module to execute. If any."""
         try:
             module = importlib.import_module(self.module_name)
             return module

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 4
+MICRO = 26
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

tomwer-1.3.26-py3.11-nspkg.pth

@@ -0,0 +1 @@
+import sys, types, os;p = os.path.join(sys._getframe(1).f_locals['sitedir'], *('orangecontrib',));importlib = __import__('importlib.util');__import__('importlib.machinery');m = sys.modules.setdefault('orangecontrib', importlib.util.module_from_spec(importlib.machinery.PathFinder.find_spec('orangecontrib', [os.path.dirname(p)])));m = m or sys.modules.setdefault('orangecontrib', types.ModuleType('orangecontrib'));mp = (m or []) and m.__dict__.setdefault('__path__',[]);(p not in mp) and mp.append(p)

{tomwer-1.3.4.dist-info → tomwer-1.3.26.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.4
+Version: 1.3.26
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit
@@ -18,49 +18,24 @@ Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: setuptools
 Requires-Dist: psutil
 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: tomoscan <2.1,>=2.0.0a11
+Requires-Dist: nxtomo <1.3,>=1.2.3rc1
+Requires-Dist: nxtomomill <1.1,>=1.0dev
 Requires-Dist: processview >=1.3
 Requires-Dist: ewoks >=0.1.1
-Requires-Dist: ewoksorange ==0.6
+Requires-Dist: ewoksorange <0.7,>=0.6
 Requires-Dist: sluurp >=0.3.3
 Requires-Dist: packaging
 Requires-Dist: flufl-lock
-Requires-Dist: pyunitsystem >=1.1.0
-Provides-Extra: _dev_spec
-Requires-Dist: black ; extra == '_dev_spec'
-Requires-Dist: flake8 ; extra == '_dev_spec'
-Requires-Dist: timeout-decorator ; extra == '_dev_spec'
-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: 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: lxml ; extra == '_full_base'
-Requires-Dist: werkzeug ; extra == '_full_base'
-Requires-Dist: json-rpc ; extra == '_full_base'
-Requires-Dist: scipy ; extra == '_full_base'
-Requires-Dist: Pillow ; extra == '_full_base'
-Requires-Dist: glymur ; extra == '_full_base'
-Requires-Dist: resource ; extra == '_full_base'
-Requires-Dist: tifffile ; extra == '_full_base'
-Requires-Dist: hdf5plugin ; extra == '_full_base'
-Requires-Dist: pyicat-plus ; extra == '_full_base'
+Requires-Dist: pyunitsystem <2.0,>=1.1.0
 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: rsyncmanager ; extra == 'dev'
 Requires-Dist: graypy ; extra == 'dev'
@@ -77,15 +52,13 @@ Requires-Dist: tifffile ; extra == 'dev'
 Requires-Dist: hdf5plugin ; extra == 'dev'
 Requires-Dist: pyicat-plus ; extra == 'dev'
 Requires-Dist: nabu[full] >=2023.3.1dev ; extra == 'dev'
-Requires-Dist: pycuda ; extra == 'dev'
+Requires-Dist: pycuda <2024.1.1 ; extra == 'dev'
 Requires-Dist: scikit-cuda ; extra == 'dev'
 Requires-Dist: black ; extra == 'dev'
 Requires-Dist: flake8 ; extra == 'dev'
 Requires-Dist: timeout-decorator ; extra == 'dev'
 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: rsyncmanager ; extra == 'dev_no_cuda'
 Requires-Dist: graypy ; extra == 'dev_no_cuda'
@@ -101,14 +74,17 @@ 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 >=2023.3.1dev ; extra == 'dev_no_cuda'
+Requires-Dist: nabu <2024.2,>=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'
 Requires-Dist: pyopencl ; extra == 'dev_no_cuda'
+Provides-Extra: dev_spec
+Requires-Dist: black ; extra == 'dev_spec'
+Requires-Dist: flake8 ; extra == 'dev_spec'
+Requires-Dist: timeout-decorator ; extra == 'dev_spec'
+Requires-Dist: pyopencl ; extra == 'dev_spec'
 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: rsyncmanager ; extra == 'doc'
 Requires-Dist: graypy ; extra == 'doc'
@@ -124,7 +100,7 @@ Requires-Dist: resource ; extra == 'doc'
 Requires-Dist: tifffile ; extra == 'doc'
 Requires-Dist: hdf5plugin ; extra == 'doc'
 Requires-Dist: pyicat-plus ; extra == 'doc'
-Requires-Dist: nabu >=2023.3.1dev ; extra == 'doc'
+Requires-Dist: nabu <2024.2,>=2023.3.1dev ; extra == 'doc'
 Requires-Dist: Sphinx >=4.0.0 ; extra == 'doc'
 Requires-Dist: nbsphinx ; extra == 'doc'
 Requires-Dist: pandoc ; extra == 'doc'
@@ -133,8 +109,6 @@ 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: rsyncmanager ; extra == 'full'
 Requires-Dist: graypy ; extra == 'full'
@@ -151,11 +125,25 @@ Requires-Dist: tifffile ; extra == 'full'
 Requires-Dist: hdf5plugin ; extra == 'full'
 Requires-Dist: pyicat-plus ; extra == 'full'
 Requires-Dist: nabu[full] >=2023.3.1dev ; extra == 'full'
-Requires-Dist: pycuda ; extra == 'full'
+Requires-Dist: pycuda <2024.1.1 ; extra == 'full'
 Requires-Dist: scikit-cuda ; extra == 'full'
+Provides-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: lxml ; extra == 'full_base'
+Requires-Dist: werkzeug ; extra == 'full_base'
+Requires-Dist: json-rpc ; extra == 'full_base'
+Requires-Dist: scipy ; extra == 'full_base'
+Requires-Dist: Pillow ; extra == 'full_base'
+Requires-Dist: glymur ; extra == 'full_base'
+Requires-Dist: resource ; extra == 'full_base'
+Requires-Dist: tifffile ; extra == 'full_base'
+Requires-Dist: hdf5plugin ; extra == 'full_base'
+Requires-Dist: pyicat-plus ; extra == 'full_base'
 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: rsyncmanager ; extra == 'full_no_cuda'
 Requires-Dist: graypy ; extra == 'full_no_cuda'
@@ -171,10 +159,8 @@ 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 >=2023.3.1dev ; extra == 'full_no_cuda'
+Requires-Dist: nabu <2024.2,>=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: rsyncmanager ; extra == 'full_no_nabu'
 Requires-Dist: graypy ; extra == 'full_no_nabu'