tomwer 1.3.5__py3-none-any.whl → 1.3.6__py3-none-any.whl

tomwer/core/process/control/datalistener/datalistener.py

@@ -37,7 +37,7 @@ import typing
 from ewokscore.task import Task as EwoksTask
 from nxtomomill import converter as nxtomomill_converter
 from silx.io.utils import h5py_read_dataset
-from tomoscan.io import HDF5File
+from silx.io.utils import open as open_hdf5
 
 import tomwer.version
 from tomwer.core import settings
@@ -229,7 +229,7 @@ class DataListener(BaseProcessInfo):
         """Return the list of scans dir for this bliss_file / entry"""
 
         def get_scan_indexes():
-            with HDF5File(bliss_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+            with open_hdf5(bliss_file) as h5f:
                 entry_node = h5f[entry]
                 if _SCAN_NUMBER_PATH in entry_node:
                     return h5py_read_dataset(entry_node[_SCAN_NUMBER_PATH])
@@ -254,7 +254,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -269,7 +269,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+        with open_hdf5(process_file) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -311,7 +311,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -326,7 +326,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+        with open_hdf5(process_file) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -360,7 +360,7 @@ class DataListener(BaseProcessInfo):
         """Return the proposal file of the experimentation if registred by the
         data listener"""
         if entry is None:
-            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -375,7 +375,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+        with open_hdf5(process_file) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -410,7 +410,7 @@ class DataListener(BaseProcessInfo):
         specific sequence data
         """
         if entry is None:
-            with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = BaseProcessInfo._get_process_nodes(
                     root_node=h5f, process=DataListener
                 )
@@ -425,7 +425,7 @@ class DataListener(BaseProcessInfo):
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+        with open_hdf5(process_file) as h5f:
             dl_nodes = BaseProcessInfo._get_process_nodes(
                 root_node=h5f[entry], process=DataListener
             )
@@ -503,7 +503,7 @@ class DataListener(BaseProcessInfo):
         # write
         def sequence_is_finished():
             try:
-                with HDF5File(bliss_file, "r", swmr=DataListener.SWMR_MODE) as h5f:
+                with open_hdf5(bliss_file) as h5f:
                     end_scan_path = "/".join((entry, "end_time"))
                     return end_scan_path in h5f
             except Exception:

tomwer/core/process/reconstruction/axis/axis.py

@@ -76,7 +76,7 @@ else:
     has_composite_cor_finder = True
 from silx.io.url import DataUrl
 from silx.io.utils import h5py_read_dataset
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
 
 _logger = logging.getLogger(__name__)
 if not has_composite_cor_finder:
@@ -1164,7 +1164,7 @@ class AxisTask(
         :return:
         """
         if entry is None:
-            with HDF5File(process_file, "r", swmr=get_swmr_mode()) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = AxisTask._get_process_nodes(root_node=h5f, process=AxisTask)
                 if len(entries) == 0:
                     _logger.info("unable to find a Axis process in %s" % process_file)
@@ -1175,7 +1175,7 @@ class AxisTask(
                     entry = list(entries.keys())[0]
                     _logger.info("take %s as default entry" % entry)
 
-        with HDF5File(process_file, "r", swmr=get_swmr_mode()) as h5f:
+        with open_hdf5(process_file) as h5f:
             axis_nodes = AxisTask._get_process_nodes(
                 root_node=h5f[entry], process=AxisTask
             )

tomwer/core/process/reconstruction/darkref/darkrefscopy.py

@@ -39,6 +39,7 @@ from typing import Union
 
 from silx.io.dictdump import dicttoh5, h5todict
 from silx.io.url import DataUrl
+from silx.io.utils import open as open_hdf5
 from tomoscan.esrf.scan.utils import (
     copy_h5_dict_darks_to,
     copy_h5_dict_flats_to,
@@ -297,7 +298,7 @@ class DarkRefsCopy(DarkRefsTask):
         if not os.path.exists(self._save_file):
             return False
         else:
-            with HDF5File(self._save_file, mode="r") as h5f:
+            with open_hdf5(self._save_file) as h5f:
                 return self._flats_url.data_path() in h5f
 
     def has_dark_stored(self) -> bool:
@@ -309,7 +310,7 @@ class DarkRefsCopy(DarkRefsTask):
         if not os.path.exists(self._save_file):
             return False
         else:
-            with HDF5File(self._save_file, mode="r") as h5f:
+            with open_hdf5(self._save_file) as h5f:
                 return self._darks_url.data_path() in h5f
 
     def contains_dark(self, scan: TomwerScanBase) -> bool:

tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -43,9 +43,10 @@ import sys
 
 import numpy
 from silx.io.url import DataUrl
+from silx.io.utils import open as open_hdf5
 from sluurp.executor import submit as submit_to_slurm_cluster
 from sluurp.job import SBatchScriptJob
-from tomoscan.io import HDF5File, get_swmr_mode
+from tomoscan.io import HDF5File
 from tomoscan.normalization import Method as INormMethod
 from tomoscan.identifier import VolumeIdentifier
 
@@ -581,9 +582,7 @@ class _NabuBaseReconstructor:
                     # if an url exists insure we can access it
                     dataset_url = DataUrl(path=dataset_url)
                     if os.path.exists(dataset_url.file_path()):
-                        with HDF5File(
-                            dataset_url.file_path(), mode="r", swmr=get_swmr_mode()
-                        ) as h5f:
+                        with open_hdf5(dataset_url.file_path()) as h5f:
                             if dataset_url.data_path() not in h5f:
                                 dataset_url = None
                     else:

tomwer/core/process/reconstruction/nabu/nabuslices.py

@@ -35,6 +35,7 @@ import os
 import gc
 from tomwer.io.utils import format_stderr_stdout
 from silx.utils.deprecation import deprecated, deprecated_warning
+from silx.io.utils import open as open_hdf5
 
 from processview.core.manager.manager import ProcessManager, DatasetState
 
@@ -84,7 +85,6 @@ from processview.core.superviseprocess import SuperviseProcess
 from silx.io.dictdump import h5todict
 from silx.io.utils import h5py_read_dataset
 from silx.utils.enum import Enum as _Enum
-from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.core.process.task import Task
 from tomwer.core.scan.edfscan import EDFTomoScan
@@ -494,7 +494,7 @@ class NabuSlicesTask(
         :rtype:dict
         """
         if entry is None:
-            with HDF5File(process_file, "r", swmr=get_swmr_mode()) as h5f:
+            with open_hdf5(process_file) as h5f:
                 entries = NabuSlicesTask._get_process_nodes(
                     root_node=h5f, process=NabuSlicesTask
                 )
@@ -510,7 +510,7 @@ class NabuSlicesTask(
         configuration_path = None
         res = {}
 
-        with HDF5File(process_file, "r", swmr=get_swmr_mode()) as h5f:
+        with open_hdf5(process_file) as h5f:
             nabu_nodes = NabuSlicesTask._get_process_nodes(
                 root_node=h5f[entry], process=NabuSlicesTask
             )
@@ -845,7 +845,7 @@ class SingleSliceRunner(_NabuBaseReconstructor):
             basename, _ = os.path.splitext(scan.master_file)
             basename = os.path.basename(basename)
             try:
-                with HDF5File(scan.master_file, mode="r", swmr=get_swmr_mode()) as h5f:
+                with open_hdf5(scan.master_file) as h5f:
                     if len(h5f.keys()) > 1:
                         # if there is more than one entry in the file append the entry name to the file basename
                         basename = "_".join((basename, scan.entry.lstrip("/")))

tomwer/core/process/reconstruction/nabu/nabuvolume.py

@@ -43,10 +43,9 @@ from processview.core.manager.manager import ProcessManager, DatasetState
 from processview.core.superviseprocess import SuperviseProcess
 
 from silx.io.utils import h5py_read_dataset
+from silx.io.utils import open as open_hdf5
 from tomwer.core.utils.deprecation import deprecated_warning
 
-from tomoscan.io import HDF5File, get_swmr_mode
-
 from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.nabu.plane import NabuPlane
@@ -354,9 +353,7 @@ class VolumeRunner(_NabuBaseReconstructor):
             basename = os.path.basename(basename)
             try:
                 # if there is more than one entry in the file append the entry name to the file basename
-                with HDF5File(
-                    self.scan.master_file, mode="r", swmr=get_swmr_mode()
-                ) as h5f:
+                with open_hdf5(self.scan.master_file) as h5f:
                     if len(h5f.keys()) > 1:
                         basename = "_".join((basename, self.scan.entry.strip("/")))
             except Exception:

tomwer/core/process/task.py

@@ -46,7 +46,8 @@ from ewokscore.task import Task as _EwoksTask
 from ewokscore.taskwithprogress import TaskWithProgress as _EwoksTaskWithProgress
 from silx.io.dictdump import dicttoh5, h5todict
 from silx.io.utils import h5py_read_dataset
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
+from tomoscan.io import HDF5File
 from tomwer.core.utils.locker import FileLockerManager
 
 
@@ -376,7 +377,7 @@ class BaseProcessInfo:
         :rtype: list
         """
         # retrieve process to load
-        with HDF5File(process_file, mode="r", swmr=get_swmr_mode()) as h5f:
+        with open_hdf5(process_file) as h5f:
             if entry is None:
                 if len(h5f.keys()) > 0:
                     root = h5f[list(h5f.keys())[0]]

tomwer/core/process/test/test_data_transfer.py

@@ -42,7 +42,8 @@ from nxtomomill.converter import from_h5_to_nx
 from nxtomomill.io.config.hdf5config import TomoHDF5Config
 from nxtomo.nxobject.nxdetector import ImageKey
 
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
+from tomoscan.io import HDF5File
 from tomoscan.validator import is_valid_for_reconstruction
 
 from tomwer.core.process.control.datalistener import DataListener
@@ -335,9 +336,9 @@ class NXTomoDataTransferBase(unittest.TestCase):
         dst_scan = process.outputs.data
         assert dst_scan.master_file != self.nexus_file_path
         assert is_valid_for_reconstruction(dst_scan, check_values=True)
-        with HDF5File(src_scan.master_file, mode="r", swmr=get_swmr_mode()) as h5s_src:
+        with open_hdf5(src_scan.master_file) as h5s_src:
             src_dataset = h5s_src["entry0000/detector/data"][...]
-        with HDF5File(dst_scan.master_file, mode="r", swmr=get_swmr_mode()) as h5s_dst:
+        with open_hdf5(dst_scan.master_file) as h5s_dst:
             dst_dataset = h5s_dst["entry0000/detector/data"][...]
         assert numpy.array_equal(src_dataset, dst_dataset)
 

tomwer/core/scan/blissscan.py

@@ -54,7 +54,7 @@ import logging
 from typing import Optional
 
 from silx.io.utils import h5py_read_dataset
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
 
 _logger = logging.getLogger(__name__)
 
@@ -203,7 +203,7 @@ class BlissScan:
                     return True
             return False
 
-        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+        with open_hdf5(file_path) as h5s:
             if not isinstance(h5s, h5py.Group) or not isinstance(
                 h5s[entry], h5py.Group
             ):
@@ -227,7 +227,7 @@ class BlissScan:
             return tuple()
         else:
             res = []
-            with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(file_path) as h5s:
                 for entry in h5s:
                     if BlissScan.is_bliss_valid_entry(file_path=file_path, entry=entry):
                         res.append(entry)

tomwer/core/scan/nxtomoscan.py

@@ -40,12 +40,12 @@ from urllib.parse import urlparse
 
 import h5py
 from processview.core.dataset import DatasetIdentifier
+from silx.io.utils import open as open_hdf5
 from tomoscan.esrf.identifier.hdf5Identifier import (
     NXtomoScanIdentifier as _NXtomoScanIdentifier,
 )
 from tomoscan.esrf.identifier.url_utils import UrlSettings, split_path, split_query
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan as _tsNXtomoScan
-from tomoscan.io import HDF5File, get_swmr_mode
 from nxtomo.nxobject.nxdetector import ImageKey
 
 from tomwer.utils import docstring
@@ -424,7 +424,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
             return tuple()
         else:
             res = []
-            with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(file_path) as h5s:
                 for entry_name, node in h5s.items():
                     if isinstance(node, h5py.Group):
                         if NXtomoScan.entry_is_nx_tomo(node):

tomwer/core/scan/scanbase.py

@@ -40,8 +40,9 @@ import functools
 import numpy
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
+from silx.io.utils import open as open_hdf5
+
 from tomoscan.identifier import VolumeIdentifier
-from tomoscan.io import HDF5File, get_swmr_mode
 from tomoscan.normalization import IntensityNormalization
 from tomoscan.volumebase import VolumeBase
 from tomoscan.identifier import BaseIdentifier
@@ -131,7 +132,7 @@ class TomwerScanBase(TomwerObject):
             and self.process_file is not None
             and os.path.exists(self.process_file)
         ):
-            with HDF5File(self.process_file, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(self.process_file) as h5s:
                 self._process_index = len(h5s.items())
         else:
             self._process_index = 0
@@ -756,7 +757,7 @@ class TomwerScanBase(TomwerObject):
         from tomwer.core.process.task import Task
 
         if os.path.exists(self.process_file):
-            with HDF5File(self.process_file, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(self.process_file) as h5s:
                 if not hasattr(self, "entry"):
                     entry = "entry"
                 else:
@@ -864,9 +865,7 @@ def _get_reconstructed_single_file_volume(
 
                 if check_url is True:
                     try:
-                        with HDF5File(
-                            os.path.abspath(file_), "r", swmr=get_swmr_mode()
-                        ) as h5f:
+                        with open_hdf5(os.path.abspath(file_)) as h5f:
                             if entry not in h5f:
                                 logger.info("{volume} does not exists")
                                 return None

tomwer/gui/control/reducedarkflatselector.py

@@ -8,11 +8,11 @@ from silx.gui import qt
 from silx.gui.plot import Plot2D
 from silx.io.dictdump import h5todict
 from silx.io.url import DataUrl
+from silx.io.utils import open as open_hdf5
 from silx.gui.dialog.DataFileDialog import DataFileDialog
 
 from tomoscan.esrf.scan.utils import cwd_context
 from tomoscan.framereducer.target import REDUCER_TARGET
-from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.io.utils import get_default_directory
 
@@ -249,7 +249,7 @@ class ReduceDarkFlatSelectorTableWidget(qt.QWidget):
         if not os.path.exists(file_path):
             _logger.error(f"file doesn't exists ({file_path})")
 
-        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5f:
+        with open_hdf5(file_path) as h5f:
             entries = tuple(h5f.keys())
 
         res = []

tomwer/gui/edit/dkrfpatch.py

@@ -36,8 +36,8 @@ from silx.gui import qt
 from silx.gui.dialog.DataFileDialog import DataFileDialog
 from silx.io.url import DataUrl
 from silx.io.utils import h5py_read_dataset
+from silx.io.utils import open as open_hdf5
 from nxtomo.nxobject.nxdetector import ImageKey
-from tomoscan.io import HDF5File, get_swmr_mode
 
 import tomwer.core.utils.nxtomoutils as nxtomo_utils
 from tomwer.core.scan.nxtomoscan import NXtomoScan
@@ -83,7 +83,7 @@ class _DarkOrFlatUrl(qt.QWidget):
         url = self._redirectDataPath(url, logger=_logger)
 
         def dataset_invalid(url):
-            with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(url.file_path()) as h5s:
                 if not isinstance(h5s[url.data_path()], h5py.Dataset):
                     return True
             return False
@@ -113,7 +113,7 @@ class _DarkOrFlatUrl(qt.QWidget):
 
     def _redirectDataPath(self, url, logger=None):
         try:
-            with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(url.file_path()) as h5s:
                 node = h5s[url.data_path()]
 
                 if NXtomoScan.entry_is_nx_tomo(node):
@@ -188,7 +188,7 @@ class _DarkOrFlatUrl(qt.QWidget):
     def _getImageKey(self, url):
         # if we are on a 'detector / data dataset' then we can try to reach
         # image_key information
-        with HDF5File(url.file_path(), mode="r", swmr=get_swmr_mode()) as h5s:
+        with open_hdf5(url.file_path()) as h5s:
             dataset = h5s[url.data_path()]
             grp_parent = dataset.parent
             if grp_parent is not None and NXtomoScan.is_nxdetector(grp_parent):

tomwer/gui/edit/nxtomowarmer.py

@@ -1,9 +1,10 @@
 from typing import Optional
 import h5py
 from silx.gui import qt
+from silx.io.utils import open as open_hdf5
+
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.gui import icons
-from tomoscan.io import HDF5File, get_swmr_mode
 
 
 class NXtomoProxyWarmer(qt.QWidget):
@@ -44,7 +45,7 @@ class NXtomoProxyWarmer(qt.QWidget):
         if scan is None:
             self._activateWarning(False)
         elif isinstance(scan, NXtomoScan):
-            with HDF5File(scan.master_file, mode="r", swmr=get_swmr_mode()) as h5f:
+            with open_hdf5(scan.master_file) as h5f:
                 entry = h5f.get(
                     name=scan.entry, getclass=True, getlink=True, default=None
                 )

tomwer/gui/imagefromfile.py

@@ -34,7 +34,7 @@ import logging
 
 from silx.gui import qt
 from silx.io.url import DataUrl
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
 
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.synctools.imageloaderthread import ImageLoaderThread
@@ -71,7 +71,7 @@ class ImageFromFile(_Image):
 
                 def get_nabu_entry():
                     try:
-                        with HDF5File(_file, mode="r", swmr=get_swmr_mode()) as h5s:
+                        with open_hdf5(_file) as h5s:
                             for node in h5s:
                                 if "reconstruction" in h5s[node]:
                                     return "/".join(

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/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 3
-MICRO = 5
+MICRO = 6
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.3.5.dist-info → tomwer-1.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.5
+Version: 1.3.6
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.3.5.dist-info → tomwer-1.3.6.dist-info}/RECORD

@@ -1,4 +1,4 @@
-tomwer-1.3.5-py3.11-nspkg.pth,sha256=xeeGR3TjdoVxdFeF6T-zSwZWh6Et--EYuPWu67LxL_c,574
+tomwer-1.3.6-py3.11-nspkg.pth,sha256=xeeGR3TjdoVxdFeF6T-zSwZWh6Et--EYuPWu67LxL_c,574
 orangecontrib/tomwer/__init__.py,sha256=B4DXy1gY_wXmNYa2aOfapmJb2mEuCAjoaNEGnpBs70g,148
 orangecontrib/tomwer/state_summary.py,sha256=5_dPzweL3r0ye4ZfJo6IV2ThJI8fQhWoO2ySdJJajj8,1711
 orangecontrib/tomwer/orange/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -220,7 +220,7 @@ orangecontrib/tomwer/widgets/visualization/icons/volumeviewer.svg,sha256=2uT9_px
 tomwer/__init__.py,sha256=82Jp1abyG4UWdGuT4nNU7LxaUV6xxkOte5pIz3w69Do,1745
 tomwer/__main__.py,sha256=jsDfWA2yl5am0dHQVkYwlKLxxqKNont6VDF-LusuawE,8575
 tomwer/utils.py,sha256=EgVwJ5CQVjoBvcKNwyVoXv_P4ciI11oxb8fNyy82Lck,8465
-tomwer/version.py,sha256=7RnYG3T8V7-HCuyqmXQHZ9FNoUnZS9FQvPROmBSP_fc,4386
+tomwer/version.py,sha256=uL9QPJPqCFjLS5OtVGnrUyJmYbddVDNZ1-V5j_9cyhQ,4386
 tomwer/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/app/axis.py,sha256=Ax0wlTp9u0Ll_3ax23QP5Ck16_M9Kop7wx0hAbXrXyM,6004
 tomwer/app/canvas.py,sha256=RbQqgE7DuNjv4nGG6BNfnSevQO5_lCl7N71hGcLoxwE,1561
@@ -263,7 +263,7 @@ tomwer/core/log/logger.py,sha256=KDHLUbaVx3hOuIk8WmzS61x1IkYgAZJ97nVYUI5-PTU,409
 tomwer/core/log/processlog.py,sha256=0XmoKVUpHjxvaOFEi56eqF1edHPzCfsCmjdMMZP2sxs,3697
 tomwer/core/process/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/output.py,sha256=UmOczI3GYNXm79B_1B3DInrXZqerhMF98Hru4KcgP1o,1562
-tomwer/core/process/task.py,sha256=2N7qH1t5GDd6ooXq9srXWm8mE8Th9a_Q2r-nvaZ-Mmo,15705
+tomwer/core/process/task.py,sha256=3_AuZGwUoLLUw5B8ZwYt0cDFeZ_g1VtTBta573tiODQ,15703
 tomwer/core/process/utils.py,sha256=LIzKwucEq6IqQ7L8L70UgDBaE9F29h_gjipQsa1RFo8,4010
 tomwer/core/process/cluster/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/cluster/supervisor.py,sha256=sStffXsjWEYaAF0yL03igtLflRnmr3zJzHRWGidwHas,1755
@@ -284,7 +284,7 @@ tomwer/core/process/control/tomoobjserie.py,sha256=L--pjgc0P-2wCul9KERwT4jeq45Rk
 tomwer/core/process/control/volumeselector.py,sha256=0uv1Q8k5Ms1h_iU-ldhb-Y35xsy1kHwQrbUQguV5M_A,370
 tomwer/core/process/control/volumesymlink.py,sha256=lcHS5eJv5lr72BAXrTe0QfwQw8amXIu0lPRsPdL6o_o,7626
 tomwer/core/process/control/datalistener/__init__.py,sha256=gSEeJEDX8E-8HzY7tmPc32QKfqSZHG4Ad06IxDrzOWo,52
-tomwer/core/process/control/datalistener/datalistener.py,sha256=_2-PKCdiMe58W5mO5eOEsNGF1FuVzx1Q7tNWXSa8n2o,22406
+tomwer/core/process/control/datalistener/datalistener.py,sha256=Je1zillD907UEacwMoFpSVJ6AzzgOEKKaMCjngBERpI,22087
 tomwer/core/process/control/datalistener/rpcserver.py,sha256=BAIpBqovcxr5R-F144uvAYYUVgqSiXeDRYuw-ZeVgF8,11104
 tomwer/core/process/control/datawatcher/__init__.py,sha256=F9d_bGOr5iAPEfnKaf5XOEwQSR1wZp_wkzcDYNSuin4,50
 tomwer/core/process/control/datawatcher/datawatcher.py,sha256=oU0nBmn_-cv_f8r-dTQM4I8QT5XPxLuQ6s4yLkf_PEk,16822
@@ -312,22 +312,22 @@ tomwer/core/process/reconstruction/output.py,sha256=JxtQ-ky2rPjTet2kYtIlzqnfj9E7
 tomwer/core/process/reconstruction/paramsbase.py,sha256=YhCqZwZCM632WdLlLHJVEwBHnXwbBf7CoLA3jESxOFE,7725
 tomwer/core/process/reconstruction/axis/__init__.py,sha256=VSQkN6M6JvM_c55OiboNyJUW8Zs1wkkQgv1JYmzvIr8,80
 tomwer/core/process/reconstruction/axis/anglemode.py,sha256=sOkuTqO8sR8xd_tEwZHj-o1TA1z33AmwwZbrPnuYqmI,1896
-tomwer/core/process/reconstruction/axis/axis.py,sha256=CfHrPLUxbPgxmLbMOe5Mw479Geu0q4yo2i3YWrOnBls,42779
+tomwer/core/process/reconstruction/axis/axis.py,sha256=nkBkDjB5yGkxRNWtjnFrixwOE_qCx5iNloIpWEZne3M,42723
 tomwer/core/process/reconstruction/axis/mode.py,sha256=CvYf-Mat3Vc6Ki1RSUQl4_Z02OKdmXUmpknnLmUgz5k,6750
 tomwer/core/process/reconstruction/axis/params.py,sha256=y1RgFAk1wiJMeueSNJH5enUnUDxw-jsb9_JF_XxSYks,33185
 tomwer/core/process/reconstruction/axis/projectiontype.py,sha256=0w_NZ0N95iInHuEQCIxJIxt7K-YpCUo2fZ-_vhZ6D7Q,1543
 tomwer/core/process/reconstruction/darkref/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/reconstruction/darkref/darkrefs.py,sha256=gbRq1IJ-9fxD71684wajQj3D_M9G6chm7ahZsjxTmpM,20862
-tomwer/core/process/reconstruction/darkref/darkrefscopy.py,sha256=xcc9huplaFNVud5bUAbe7hxdg0B7YG4R2NWuytR7arM,13250
+tomwer/core/process/reconstruction/darkref/darkrefscopy.py,sha256=6wEBs7yBZHeEADxDLZ-jYTxaeOBJCJacqfskkr1-ytE,13276
 tomwer/core/process/reconstruction/darkref/params.py,sha256=Pnl8XJ4et-u169wzUdhB8_woBEXPXtrGPLZEbXSwZDQ,10080
 tomwer/core/process/reconstruction/darkref/settings.py,sha256=35jliuOIjMKTOJjgn4uiotcDEr6RskpLHfRWWLm76dc,188
 tomwer/core/process/reconstruction/nabu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/reconstruction/nabu/castvolume.py,sha256=qk5bNGcPXylEXfHE3eB6gIh2_Bh-ehtq4Z1Ok8hXd5s,10239
 tomwer/core/process/reconstruction/nabu/helical.py,sha256=gauUkoPiShvnvMQrCQXv28g0yLe-GceML5kYMSXmNIg,1997
-tomwer/core/process/reconstruction/nabu/nabucommon.py,sha256=tKbwkEcheecG0hLyl7seZVHvZwsQpzkFgnAmjUs03OE,24484
+tomwer/core/process/reconstruction/nabu/nabucommon.py,sha256=3OyyDjBfdrEF4ctXo6LBH-WeyrKh24j6sJUocA7TwXw,24428
 tomwer/core/process/reconstruction/nabu/nabuscores.py,sha256=UtTpMF_NZhmz_q8zvBZj6W91cNxYEA3BckWL5GRmCag,25702
-tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=bIk3MAY72tNnmOpbg-REXiFdOBLtC1kWWZd8a5aPp5M,38818
-tomwer/core/process/reconstruction/nabu/nabuvolume.py,sha256=gYXQRxVhdbizz7iwh2jnio6Sy_aWXCiMO-mb3rTci5Y,21990
+tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=lDgGGRQ2xABu9TXs8m-aeyP_jCs3m2WGF75MRd58xm0,38731
+tomwer/core/process/reconstruction/nabu/nabuvolume.py,sha256=z7nyfXhMrp0Q3hAN3NYw5rvvjdgU-ZQQ7kMD3bEiFcU,21916
 tomwer/core/process/reconstruction/nabu/plane.py,sha256=Cgzth77M0pFgLDULmvmPj4bqFm5MvIMJ7Ien8mRqLsE,134
 tomwer/core/process/reconstruction/nabu/settings.py,sha256=JpHKf0smiXeWC8i9Mj7h3g67teJ3Gqycd-Uwg2yzGOQ,2279
 tomwer/core/process/reconstruction/nabu/target.py,sha256=_Z4gViprjR3Vm4KASqsASStLA9GM1wTyoi3Pg0PUSeg,1481
@@ -364,7 +364,7 @@ tomwer/core/process/test/test_axis.py,sha256=So1e1WnVuhvFCv5wT5dftZ9JFsVsc8uR0Qe
 tomwer/core/process/test/test_conditions.py,sha256=7yKYB_Bg6dQqblA3lGD4eESegDX6MU2AzmUahWTzmdI,3464
 tomwer/core/process/test/test_dark_and_flat.py,sha256=XyfTtZAH-qleMUwVhaDkpbkxIeqWlgYXMeLVipc0spI,15444
 tomwer/core/process/test/test_data_listener.py,sha256=ab_FZM7f-lXzQ6eMY-4aCFyTUqWuexZKV_tiRaPVfzE,3696
-tomwer/core/process/test/test_data_transfer.py,sha256=d8aZkH3rhKlUUvvaxvEJRTeMXNExdpvUHMvs0-f6vI8,15452
+tomwer/core/process/test/test_data_transfer.py,sha256=6vHQTv4C6pI5XTGTwQCG4U0OQKfR42HviX5frBMsQGE,15419
 tomwer/core/process/test/test_data_watcher.py,sha256=y0FpUqxlpKZu7OhuwlxeLPX5ESPXj_2m2lKjEWrVCV4,3138
 tomwer/core/process/test/test_nabu.py,sha256=mMaMNS4Sp-4On6ZDcuNVajQPTiO5kFy84z9p7_pUhzw,19621
 tomwer/core/process/test/test_normalization.py,sha256=m9hSFi88Q2IGiyNb9emGsS5HOBx9HulJsejUjO0x5Mo,4014
@@ -380,13 +380,13 @@ tomwer/core/process/visualization/sinogramviewer.py,sha256=VPkea5-DiVv_fCvg_UqBo
 tomwer/core/process/visualization/slicestack.py,sha256=0388rNQBDu_ihJ_vGT7EtwiGPlHf-yJDVBK8VCLXsEo,1625
 tomwer/core/process/visualization/volumeviewer.py,sha256=h2_LOfx0PNJaBK0cyUDniuV1Gf7FwLsHwU3jFaAbOow,1579
 tomwer/core/scan/__init__.py,sha256=V1TPi41mS3b6jskdiNqgnKYvRHZg1x1KmEClQ3hUmu8,1392
-tomwer/core/scan/blissscan.py,sha256=sldjJdZjRgGRlGASrpTzYTBVbkEhSWJ1Vi052Zzhy34,8310
+tomwer/core/scan/blissscan.py,sha256=yfJaoYGeEKehZwKj1sfdzXU7rohxm5mbOdaORXIRI7o,8244
 tomwer/core/scan/edfscan.py,sha256=_J6NyqXkMcrD6NirLT-TmI-Le2UpdV8uy8XOmrdu9AM,22892
 tomwer/core/scan/futurescan.py,sha256=chXjteQ4_6cSyFBoCil-DeHkHGGzM-xb21xJRYLEfhI,213
 tomwer/core/scan/hdf5scan.py,sha256=P7LHxyqY9Ujg19MpYVItarKxFEy2Z_PVTh5Hi3PCXyU,980
 tomwer/core/scan/helicalmetadata.py,sha256=JRBxqHkyTe5f3FDlbIeDfN31P6Ms48SqGiFRXHuZ8sw,472
-tomwer/core/scan/nxtomoscan.py,sha256=FbWSMjWZP0tO0WyFXP-DBxiKzR2dJV7th8w5wFdi1Kw,19440
-tomwer/core/scan/scanbase.py,sha256=noq-wwEnffhJ3C1VLCMDsy3NLNIQwKdr3FWak-n3gG8,32197
+tomwer/core/scan/nxtomoscan.py,sha256=WJEO_hQTcMhgALI5KaSIQy8bGsLEeX2Po0ArUdxlqA0,19405
+tomwer/core/scan/scanbase.py,sha256=PSPeGM6mI6EacE_VUWLTUGcjhdJnY6ZpR_I4qHSHmIc,32052
 tomwer/core/scan/scanfactory.py,sha256=Ltisxo9B8j11lS_cdwUjuEH1ZjPb9nmU2KmkXxzU98I,10521
 tomwer/core/scan/scantype.py,sha256=pQjWuCy_014uK5cdb8pFAkE_EPHJvPdSo3NM8aWTo58,137
 tomwer/core/scan/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -429,7 +429,7 @@ tomwer/core/volume/volumefactory.py,sha256=sf9Mok3EG7a43OTrLAKnRw37TG_22FXY9rruX
 tomwer/gui/__init__.py,sha256=GuoK-CFwHqHBiLvvSUOAk6_SaXu7-k3SIYCfPTZFHFk,1474
 tomwer/gui/icons.py,sha256=r_UURvOe36k83iw5gQiEKt6fgdvPNbZgrUoeji_s6eE,12917
 tomwer/gui/illustrations.py,sha256=kKA_Jnj67QwwjHXW1d5x1qOgV2QWlktvEJYIDFTSJ-0,5368
-tomwer/gui/imagefromfile.py,sha256=mz0tKpWu_7Ezv5U6sYkb9840HWWqjyYhVYq0j_Yv9mo,5536
+tomwer/gui/imagefromfile.py,sha256=vE7O59deIJoUqCcm09tcGLZ99YHncqMf-xQbEkWboGo,5501
 tomwer/gui/qconfigfile.py,sha256=zkXEirFZbIyylm0usdn7dVRWvns6bRoqYTG2bs9JCTM,713
 tomwer/gui/qfolderdialog.py,sha256=lIptQ9WHU5OoViCTE5lJMctSBa_ayf0IBirKikrKudI,22761
 tomwer/gui/qlefilesystem.py,sha256=ooNqoAeQA_JKamBg-ZlJSfX-paAYcGAjNam25qXJPgA,534
@@ -459,7 +459,7 @@ tomwer/gui/control/emailnotifier.py,sha256=nbuy4cSXdSOiDTSwWhK2bbpIdq4bDpApWNs2z
 tomwer/gui/control/history.py,sha256=o7r2OiUqIPX7DsyPCI_r8XDkLowU5NajQnpbJic2rgY,4826
 tomwer/gui/control/nxtomomill.py,sha256=DI7DsO98O8h9mFcJ_1y1Kb8nD6w09at8YvJZNHR_EtE,7293
 tomwer/gui/control/observations.py,sha256=oj2OqWYwiewgsZ5vNjzrMjB-YPopYyJmaBE5df09L7c,7735
-tomwer/gui/control/reducedarkflatselector.py,sha256=UGnJEApAm8wO7pOLLeBS1unZZbqzKL2YpOyvKv6dV1I,20571
+tomwer/gui/control/reducedarkflatselector.py,sha256=hW2D69B2THZn8lIOaUQJHJ6aGIn-tHjcynEfIn4DftA,20536
 tomwer/gui/control/scanselectorwidget.py,sha256=m3uxkoG4aNPPwamiI14l82PNS8tvIiOXmKhBJiwHgjU,2356
 tomwer/gui/control/selectorwidgetbase.py,sha256=avj6dkBJaryCQYF66vXbuYbaLAjTwmcdQ1L24DcUH6I,5571
 tomwer/gui/control/singletomoobj.py,sha256=5R_Uwgp5wdDQudxG2vyyq4Nj1GjhqH0HCeo_cFS7WuI,6777
@@ -492,10 +492,10 @@ tomwer/gui/debugtools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 tomwer/gui/debugtools/datasetgenerator.py,sha256=b3VSgtzG4QyHqxbeVyXE4gX41cGwuVKJHhPWU9ZibQc,10641
 tomwer/gui/debugtools/objectinspector.py,sha256=Mva9iK4bIxHvs3CcuHboWa4kiUEMoBeuUOULfPNyNOs,2925
 tomwer/gui/edit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer/gui/edit/dkrfpatch.py,sha256=ZWsEYCsvRit7IA7oEkuOM_Tu0D4SzasQX3U1LdSsuWw,17630
+tomwer/gui/edit/dkrfpatch.py,sha256=UCXfEq3wV1x3OzEdzIzi6YxRN6SaEIZb-Yudt2YwnUs,17533
 tomwer/gui/edit/imagekeyeditor.py,sha256=NjnPdKJif9bhfPXejJuRrj2TqTTMlOxlk4mb6mSBoHw,29728
 tomwer/gui/edit/nxtomoeditor.py,sha256=1mV5EIHTclg1YxDLMncbErNwC58jEOGxjxO7I1dRzyQ,28095
-tomwer/gui/edit/nxtomowarmer.py,sha256=8CJ4apk9BHQatYFDj3FiK0Etv8YapieY8C60nGKcd-U,2383
+tomwer/gui/edit/nxtomowarmer.py,sha256=Vmsg8oUSzHpIvJVqF6xZd0aYKzPi_DDoNrGOIQbqBwU,2349
 tomwer/gui/edit/test/__init__.py,sha256=OLK9ip_LryBfM_L40MReqjvJS3wdbWP_CpnBeD1NQTA,1368
 tomwer/gui/edit/test/test_dkrf_patch.py,sha256=578ZPdVGOHls236XQqId7QqRrpdN5h3Hh8BePTlV03g,8001
 tomwer/gui/edit/test/test_image_key_editor.py,sha256=hkeiB5plRR17YD499j6_yQatuIgKLa4F4NfjWVMzhY4,5965
@@ -609,10 +609,10 @@ tomwer/gui/visualization/test/test_stacks.py,sha256=HFLwaJ4LCHKuhRjMB4FNhIrI3W96
 tomwer/gui/visualization/test/test_volumeviewer.py,sha256=Cf0EIQ8D_A9scznodWQGZfzkKgsuImzE44Q3A2e_PPs,2374
 tomwer/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/io/utils/__init__.py,sha256=SrC5etCrm-3oMkUc4PPRqSdkIwTvKdtnBTfxh35_exI,272
-tomwer/io/utils/h5pyutils.py,sha256=f4Oj00fxLKI-a6JAq_gPgiitInhcK65vFwIyYOX6I9c,3074
+tomwer/io/utils/h5pyutils.py,sha256=nSKVGHhFh2dJbEj6Ie0wPgU60HXxTctMJoTyRIpQPQs,2964
 tomwer/io/utils/raw_and_processed_data.py,sha256=XMAyMTbxB7orxHsYOPuWQd5QiGQB_xesx8bMf2KyW0g,3208
 tomwer/io/utils/tomoobj.py,sha256=PGcTc2nMDMzKGvL7u5LgIMc9MYhJwLN9yecA1gttmzE,2828
-tomwer/io/utils/utils.py,sha256=jy27AkxXOi6oreRCR-Q3pFqqSwftzfqSkaH0ZobKQ-c,10744
+tomwer/io/utils/utils.py,sha256=GnBaxTacb-vMJymiVk8onRRjJamGx0xRzbWl5yFl_fQ,10678
 tomwer/resources/__init__.py,sha256=dXxWZFKRE4ncPKzNq9BBLtjwRYmRvzzErgKhvzH_W6g,5904
 tomwer/resources/gui/icons/Imagej_icon.png,sha256=JFDzPw20pzRrf6wLBnScXEcmTVt6orXPzwPwniKeVss,1618960
 tomwer/resources/gui/icons/a.png,sha256=YrYFndLl3SUcsYNJDloU9YeJLBUkiMmgvDjDNJCMipI,3858
@@ -776,10 +776,10 @@ tomwer/tests/test_utils.py,sha256=D0rNDSK6csEOYBY_7gD-4A3jp8rYAm8L1_Xg34A9I2s,30
 tomwer/tests/utils.py,sha256=RAXx5A99WD4Vyuv_wjHBdr-Xu7UiThHRKw2eiB5GX10,107
 tomwer/third_part/WaitingOverlay.py,sha256=GnqiytcJDp_24Cmz_2nZAP5HfpL3Yh7AzR2ATIusGsg,3906
 tomwer/third_part/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer-1.3.5.dist-info/LICENSE,sha256=yR_hIZ1MfDh9x2_s23uFqBH7m5DgrBl9nJKkE37YChM,1877
-tomwer-1.3.5.dist-info/METADATA,sha256=CXAdzIqOr-504Mh_Dq4fDhzxC_DSK7-eT-fJ64Vmkew,11459
-tomwer-1.3.5.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
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