tomwer 1.3.5__tar.gz → 1.3.7__tar.gz

{tomwer-1.3.5/tomwer.egg-info → tomwer-1.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.5
+Version: 1.3.7
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/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-1.3.5 → tomwer-1.3.7}/tomwer/version.py

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

{tomwer-1.3.5 → tomwer-1.3.7/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.5
+Version: 1.3.7
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit