nxtomomill 2.2.0.dev0__tar.gz → 2.2.0.dev1__tar.gz

{nxtomomill-2.2.0.dev0/nxtomomill.egg-info → nxtomomill-2.2.0.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.2.0.dev0
+Version: 2.2.0.dev1
 Summary: applications and library to convert raw format to NXtomo format
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: 
@@ -58,7 +58,7 @@ Requires-Dist: silx>=2.0
 Requires-Dist: nxtomo>=3.1.0dev1
 Requires-Dist: pint
 Requires-Dist: packaging
-Requires-Dist: tomoscan[full]>=3.0.0dev0
+Requires-Dist: tomoscan>=3.0.0dev0
 Requires-Dist: tomobase>=0.0.0dev0
 Requires-Dist: tqdm
 Requires-Dist: pydantic

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/__main__.py

@@ -84,7 +84,7 @@ class Launcher(_Launcher):
                 replacement=deprecation_info.replacement,
                 since_version=deprecation_info.since,
             )
-        super().execute(argv=argv)
+        return super().execute(argv=argv)
 
     def print_help(self):
         """Print the help to stdout."""

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/app/h52nx.py

@@ -15,7 +15,7 @@ import logging
 from tqdm import tqdm
 
 from nxtomomill import utils
-from nxtomomill.converter import from_h5_to_nx
+from nxtomomill.converter.hdf5.hdf5converter import _H5ToNxConverter
 from nxtomomill.io.config.confighandler import (
     SETTABLE_PARAMETERS_UNITS,
     TomoHDF5ConfigHandler,
@@ -317,6 +317,20 @@ def main(argv):
         "Sometime relative link cannot be solved (GPFS vs NFS). "
         "In this case you might be forced to use absolute path.",
     )
+    parser.add_argument(
+        "--no-resolve-vds",
+        "--no-resolve-vds-links",
+        "--no_resolve_vds",
+        dest="resolve_vds",
+        action="store_false",
+        default=None,
+        help="Do not resolve external links and virtual datasets (VDS) down to "
+        "their final source when building the output NXtomo. Can speed up the "
+        "conversion for datasets with many nested links, at the cost of the "
+        "output file containing VDS pointing to other VDS instead of direct "
+        "links to the raw data. Defaults to the 'NXTOMOMILL_RESOLVE_VDS' "
+        "environment variable if set, else resolving is enabled.",
+    )
     options = parser.parse_args(argv[1:])
     if options.request_input:
         callback_det_sel = _ask_for_selecting_detector
@@ -335,9 +349,12 @@ def main(argv):
             configuration_handler.configuration.log_level
         )
         with tqdm(desc="h52nx", delay=1, bar_format="{l_bar}{bar}") as progress:
-            from_h5_to_nx(
+            converter = _H5ToNxConverter(
                 configuration=configuration_handler.configuration,
                 progress=progress,
                 input_callback=None,
                 detector_sel_callback=callback_det_sel,
             )
+            converter.convert()
+            if converter.has_failed_acquisitions:
+                return 1

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/acquisition/baseacquisition.py

@@ -31,7 +31,7 @@ from silx.io.utils import h5py_read_dataset
 
 from nxtomomill.models.h52nx.h52nx import H52nxModel
 from .utils._keys import keys_to_str_tuple
-from .utils._context import read_key, MissingValue
+from .utils._context import read_key, MissingValue, InvalidValue
 
 _ureg = pint.get_application_registry()
 _logger = logging.getLogger(__name__)
@@ -300,6 +300,7 @@ class BaseAcquisition:
                 file_path=output_file,
                 data_path=data_path,
                 use_abs_path_for_vds=self.configuration.use_abs_path_for_vds,
+                overwrite=self.configuration.overwrite,
             )
             # check rotation angle
             if nx_tomo.sample.rotation_angle is not None:
@@ -408,6 +409,11 @@ class BaseAcquisition:
                     except MissingValue:
                         # skip values containing '*DIS*'
                         continue
+                    except InvalidValue:
+                        # dataset reports an 'ERR' value: let it propagate, the
+                        # caller decides how to handle it (e.g. translations
+                        # fall back to None instead of trying other keys)
+                        raise
                     except KeyError as e:
                         _logger.info(
                             f"Cannot solve key {key}. Most likely one dataset is not there. Error is {e}"
@@ -697,7 +703,7 @@ class BaseAcquisition:
             _logger.warning(mess)
             return ([0] * n_frame) * _ureg.meter
 
-    def _get_translation_x(self, root_node, n_frame) -> pint.quantity:
+    def _get_translation_x(self, root_node, n_frame) -> pint.Quantity | None:
         """return the list of translation for each frame"""
         for grp in self._get_positioners_node(root_node), root_node:
             try:
@@ -708,6 +714,11 @@ class BaseAcquisition:
                     info_retrieve="x base translation",
                     expected_unit=_ureg.mm,
                 )
+            except InvalidValue:
+                _logger.error(
+                    f"translation x reports an 'ERR' value for {root_node.name}. Translation x will be set to None."
+                )
+                return None
             except (ValueError, KeyError):
                 pass
             else:
@@ -721,7 +732,7 @@ class BaseAcquisition:
             _logger.warning(mess)
             return ([0] * n_frame) * _ureg.meter
 
-    def _get_translation_y(self, root_node, n_frame) -> pint.quantity:
+    def _get_translation_y(self, root_node, n_frame) -> pint.Quantity | None:
         """return the list of translation for each frame"""
         for grp in self._get_positioners_node(root_node), root_node:
             try:
@@ -732,6 +743,11 @@ class BaseAcquisition:
                     info_retrieve="y base translation",
                     expected_unit=_ureg.mm,
                 )
+            except InvalidValue:
+                _logger.error(
+                    f"translation y reports an 'ERR' value for {root_node.name}. Translation y will be set to None."
+                )
+                return None
             except (ValueError, KeyError):
                 pass
             else:
@@ -748,7 +764,7 @@ class BaseAcquisition:
     @staticmethod
     def get_translation_z_frm(
         root_node, n_frame: int, configuration: H52nxModel
-    ) -> pint.Quantity:
+    ) -> pint.Quantity | None:
         for grp in BaseAcquisition._get_positioners_node(root_node), root_node:
             try:
                 z_tr, unit = BaseAcquisition._get_node_values_for_frame_array(
@@ -758,6 +774,11 @@ class BaseAcquisition:
                     info_retrieve="z translation",
                     expected_unit=_ureg.mm,
                 )
+            except InvalidValue:
+                _logger.error(
+                    f"translation z reports an 'ERR' value for {root_node.name}. Translation z will be set to None."
+                )
+                return None
             except (ValueError, KeyError):
                 pass
             else:
@@ -771,7 +792,7 @@ class BaseAcquisition:
             _logger.warning(mess)
             return ([0] * n_frame) * _ureg.meter
 
-    def _get_translation_z(self, root_node, n_frame) -> pint.Quantity:
+    def _get_translation_z(self, root_node, n_frame) -> pint.Quantity | None:
         """return the list of translation z for each frame"""
         return self.get_translation_z_frm(
             root_node=root_node,
@@ -804,7 +825,7 @@ class BaseAcquisition:
         else:
             mess += "default value will be set. (0)"
             _logger.warning(mess)
-            return 0 * _ureg.second
+            return numpy.zeros(n_frame) * _ureg.second
 
     def get_axis_scale_types(self):
         """

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/acquisition/standardacquisition.py

@@ -346,19 +346,22 @@ class StandardAcquisition(BaseAcquisition):
         image_key_control = frame_type.to_image_key_control()
         self._image_key_control.extend([image_key_control.value] * n_frame)
 
-        try:
-            solved_camera_dataset_urls = resolve_link(
-                dataset_url=camera_dataset_url,
-                dataset=data_dataset,
-                dataset_link=data_dataset_link,
-                open_mode_for_reading=self.configuration.open_mode_for_reading,
-            )
-        except OSError as e:
-            # This can happen if one fine cannot be found. In test for example where we are only using the master file
-            # and low level bliss / tango .h5 files are not existing
-            _logger.warning(
-                "Fail to solve camera dataset links and VDS. Error is %s", e
-            )
+        if self.configuration.resolve_vds:
+            try:
+                solved_camera_dataset_urls = resolve_link(
+                    dataset_url=camera_dataset_url,
+                    dataset=data_dataset,
+                    dataset_link=data_dataset_link,
+                    open_mode_for_reading=self.configuration.open_mode_for_reading,
+                )
+            except OSError as e:
+                # This can happen if one fine cannot be found. In test for example where we are only using the master file
+                # and low level bliss / tango .h5 files are not existing
+                _logger.warning(
+                    "Fail to solve camera dataset links and VDS. Error is %s", e
+                )
+                solved_camera_dataset_urls = (camera_dataset_url,)
+        else:
             solved_camera_dataset_urls = (camera_dataset_url,)
 
         n_total_frame_solved = 0

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/acquisition/tests/test_acquisition.py

@@ -3,6 +3,7 @@
 import os
 import tempfile
 
+import h5py
 import pytest
 from silx.io.url import DataUrl
 
@@ -52,6 +53,38 @@ def test_get_dataset_name_from_motor():
         get_dataset_name_from_motor(set_3, "rotation")
 
 
+@pytest.mark.parametrize("raises_error", (True, False))
+def test_translation_with_err_value(tmp_path, raises_error):
+    """
+    Test that translation x, y and z are set to None (instead of failing)
+    when the corresponding dataset reports an 'ERR' value.
+    """
+    file_path = os.path.join(tmp_path, "test.h5")
+    with HDF5File(file_path, mode="w") as h5f:
+        h5f["/entry/instrument/positioners/tx"] = "ERR"
+        h5f["/entry/instrument/positioners/ty"] = "ERR"
+        h5f["/entry/instrument/positioners/tz"] = "ERR"
+
+    config = TomoHDF5Config()
+    config.raises_error = raises_error
+    config.translation_x_keys = ("tx",)
+    config.translation_y_keys = ("ty",)
+    config.translation_z_keys = ("tz",)
+
+    url = DataUrl(file_path=file_path, data_path="/entry", scheme="silx")
+    std_acq = BaseAcquisition(
+        root_url=url,
+        configuration=config,
+        detector_sel_callback=None,
+        start_index=0,
+    )
+    with h5py.File(file_path, mode="r") as h5f:
+        root_node = h5f["/entry"]
+        assert std_acq._get_translation_x(root_node=root_node, n_frame=1) is None
+        assert std_acq._get_translation_y(root_node=root_node, n_frame=1) is None
+        assert std_acq._get_translation_z(root_node=root_node, n_frame=1) is None
+
+
 def test_frame_flips(tmp_path, monkeypatch):
     # make sure the result is obtained by using the "instrument/{active_config_tomo_detector}/data_axes" path.
     monkeypatch.setattr(

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/acquisition/utils/_context.py

@@ -163,6 +163,10 @@ class MissingValue(ValueError):
     """Raised if a dataset contains 'DIS' - not saved"""
 
 
+class InvalidValue(ValueError):
+    """Raised if a dataset contains 'ERR' - value could not be read from the hardware"""
+
+
 def read_key(
     key: str,
     node: h5py.Group,
@@ -210,6 +214,9 @@ def read_key(
         # skip values containing '*DIS*'
         if isinstance(values, str) and values == "*DIS*":
             raise MissingValue(f"dataset {dataset_name} has not been recorded")
+        # dataset reports an 'ERR' value if the hardware failed to record it
+        if isinstance(values, str) and values == "ERR":
+            raise InvalidValue(f"dataset {dataset_name} reports an 'ERR' value")
 
     first_dataset = dataset_names[0]
     result_unit = dataset_units[first_dataset] or expected_unit

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/hdf5converter.py

@@ -146,6 +146,7 @@ class _H5ToNxConverter(BaseConverter):
         self._detector_sel_callback = detector_sel_callback
         self._acquisitions = []
         self._entries_created = []
+        self._conversion_errors: list[tuple[str, Exception]] = []
         self._z_series_v2_v3: list[list[ZSeriesBaseAcquisition]] = []
         # bliss z-series for version 2 and 3. Can be used for post-processing
         self.preprocess()
@@ -176,6 +177,11 @@ class _H5ToNxConverter(BaseConverter):
     def acquisitions(self):
         return self._acquisitions
 
+    @property
+    def has_failed_acquisitions(self) -> bool:
+        """True if at least one acquisition failed to be converted (and the error was not raised, see 'raises_error')"""
+        return len(self._conversion_errors) > 0
+
     def preprocess(self):
         self._preprocess_urls()
         self._check_conversion_is_possible()
@@ -311,6 +317,7 @@ class _H5ToNxConverter(BaseConverter):
                         exc_info=e,
                     )
                     acquisition_to_nxtomo[acquisition] = None
+                    self._conversion_errors.append((root_location, e))
             else:
                 res.extend(new_entries)
                 acquisition_to_nxtomo[acquisition] = new_entries

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/tests/test_h52nx_utils.py

@@ -18,6 +18,7 @@ from nxtomomill.converter.hdf5.acquisition.utils._context import (
     update_config_keys_from_tomo_config_context,
     read_key,
     MissingValue,
+    InvalidValue,
 )
 from nxtomomill.converter.hdf5.acquisition.blisstomoconfig import TomoConfig
 from nxtomomill.converter.hdf5.acquisition.utils._keys import _Key
@@ -151,6 +152,10 @@ def read_key_datasets(tmp_path):
         f.create_dataset("missing_data/dataset9", data="*DIS*")
         f.create_dataset("missing_data/dataset10", data=numpy.random.random(10))
 
+        # Create datasets with 'ERR' (hardware failed to record the value)
+        f.create_dataset("invalid_data/dataset22", data="ERR")
+        f.create_dataset("invalid_data/dataset23", data=numpy.random.random(10))
+
         # Create datasets with coherent units (but different)
         f.create_dataset("with_coherent_units/dataset11", data=numpy.ones(10))
         f["with_coherent_units/dataset11"].attrs["unit"] = "meter"
@@ -214,6 +219,15 @@ def test_read_key(read_key_datasets, caplog):
                 expected_unit=_ureg.meter,
             )
 
+        # test with dataset reporting an 'ERR' value
+        with pytest.raises(InvalidValue):
+            read_key(
+                key="dataset22+dataset23",
+                node=h5f["invalid_data"],
+                info_retrieve="",
+                expected_unit=_ureg.meter,
+            )
+
         # test with dataset with coherent size and no unit
         quantity: pint.Quantity = read_key(
             key="dataset7+dataset8",

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/converter/hdf5/tests/test_hdf5converter.py

@@ -1415,6 +1415,171 @@ def test_id16a_use_case(tmp_path):
         transformation.transformation_values.magnitude == numpy.array([0.0])
 
 
+def test_resolve_vds_option(tmp_path, monkeypatch):
+    """
+    Test that the 'resolve_vds' configuration option correctly enables /
+    disables the resolving of external links and virtual datasets (VDS)
+    when building the camera dataset of the output NXtomo.
+    """
+    import nxtomomill.converter.hdf5.acquisition.standardacquisition as standardacquisition_module
+
+    folder = tmp_path / "output_test_resolve_vds_option"
+    folder.mkdir()
+    bliss_mock = MockBlissAcquisition(
+        n_sample=1,
+        n_sequence=1,
+        n_scan_per_sequence=2,
+        n_darks=1,
+        n_flats=1,
+        with_nx_detector_attr=True,
+        output_dir=folder,
+        detector_name="pcolinux",
+        create_tomo_config=False,
+    )
+    sample = bliss_mock.samples[0]
+
+    call_counter = {"n": 0}
+    original_resolve_link = standardacquisition_module.resolve_link
+
+    def _counting_resolve_link(*args, **kwargs):
+        call_counter["n"] += 1
+        return original_resolve_link(*args, **kwargs)
+
+    monkeypatch.setattr(
+        standardacquisition_module, "resolve_link", _counting_resolve_link
+    )
+
+    config = TomoHDF5Config()
+    config.input_file = sample.sample_file
+    config.single_file = True
+    config.sample_x_keys = ("sx",)
+    config.sample_y_keys = ("sy",)
+    config.translation_x_keys = ("tx",)
+
+    # by default (and with 'resolve_vds' explicitly set to True) links / VDS are resolved
+    config.resolve_vds = True
+    config.output_file = str(tmp_path / "output_resolve_vds_true.nx")
+    converter.from_h5_to_nx(configuration=config)
+    assert call_counter["n"] > 0
+    assert os.path.exists(config.output_file)
+
+    # disabling 'resolve_vds' must skip the resolving step entirely
+    call_counter["n"] = 0
+    config.resolve_vds = False
+    config.output_file = str(tmp_path / "output_resolve_vds_false.nx")
+    converter.from_h5_to_nx(configuration=config)
+    assert call_counter["n"] == 0
+    assert os.path.exists(config.output_file)
+
+
+def test_single_file_and_overwrite_from_cli(tmp_path):
+    """
+    Test that the `--single-file` and `--overwrite` options provided from
+    the CLI are correctly propagated down to the NXtomo saving step.
+    """
+    folder = tmp_path / "output_test_single_file_and_overwrite_from_cli"
+    folder.mkdir()
+    bliss_mock = MockBlissAcquisition(
+        n_sample=1,
+        n_sequence=1,
+        n_scan_per_sequence=2,
+        n_darks=1,
+        n_flats=1,
+        with_nx_detector_attr=True,
+        output_dir=folder,
+        detector_name="pcolinux",
+        create_tomo_config=False,
+    )
+    sample = bliss_mock.samples[0]
+    output_file = sample.sample_file.replace(".h5", ".nx")
+
+    config = H52nxModel()
+    config.input_file = sample.sample_file
+    config.output_file = output_file
+    config.single_file = True
+    config.request_input = False
+    config.raises_error = True
+    config.overwrite = False
+    config.sample_x_keys = ("sx",)
+    config.sample_y_keys = ("sy",)
+    config.translation_x_keys = ("tx",)
+
+    config_file = tmp_path / "config.cfg"
+    config.to_cfg_file(file_path=str(config_file))
+
+    cmd = (
+        sys.executable,
+        "-m",
+        "nxtomomill",
+        "h52nx",
+        sample.sample_file,
+        output_file,
+        "--config",
+        config_file,
+    )
+
+    # first call creates the output file
+    assert subprocess.call(cmd, cwd=tmp_path) == 0  # nosec B603
+    assert os.path.exists(output_file)
+
+    # calling it again without `--overwrite` must fail as the output file already exists
+    # and 'overwrite' is set to False in the configuration
+    assert subprocess.call(cmd, cwd=tmp_path) != 0  # nosec B603
+
+    # calling it again with `--overwrite` provided from the CLI must succeed: the option must be
+    # forwarded to the NXtomo saving step even in `--single-file` mode
+    assert subprocess.call((*cmd, "--overwrite"), cwd=tmp_path) == 0  # nosec B603
+
+
+def test_cli_exit_code_on_failed_entry(tmp_path):
+    """
+    Test that the CLI exits with a non-zero status code when an entry fails
+    to be converted, even though 'raises_error' is left to its default value
+    (False), in which case the error is logged and the conversion carries on
+    with the other entries instead of raising.
+    """
+    folder = tmp_path / "output_test_cli_exit_code_on_failed_entry"
+    folder.mkdir()
+    bliss_mock = MockBlissAcquisition(
+        n_sample=1,
+        n_sequence=1,
+        n_scan_per_sequence=2,
+        n_darks=1,
+        n_flats=1,
+        with_nx_detector_attr=True,
+        output_dir=folder,
+        detector_name="pcolinux",
+        create_tomo_config=False,
+    )
+    sample = bliss_mock.samples[0]
+    output_file = sample.sample_file.replace(".h5", ".nx")
+
+    cmd = (
+        sys.executable,
+        "-m",
+        "nxtomomill",
+        "h52nx",
+        sample.sample_file,
+        output_file,
+        "--single-file",
+        "--no-input",
+        "--sample_x_keys",
+        "sx",
+        "--sample_y_keys",
+        "sy",
+    )
+
+    # first call creates the output file and must succeed
+    assert subprocess.call(cmd, cwd=tmp_path) == 0  # nosec B603
+    assert os.path.exists(output_file)
+
+    # calling it again (without `--overwrite` nor `--raises-error`) makes the
+    # entry conversion fail internally (it is logged and the conversion is
+    # not interrupted), the CLI must still report the failure through its
+    # exit code
+    assert subprocess.call(cmd, cwd=tmp_path) != 0  # nosec B603
+
+
 def test_warning(tmp_path, caplog):
     """Test that the application raises a warning if bliss acquisition has 'end_reason' different than 'SUCCESS'"""
     config = TomoHDF5Config()

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/io/config/confighandler.py

@@ -153,6 +153,7 @@ class TomoHDF5ConfigHandler:
             "alignment_titles",
             "open_mode_for_reading",
             "output_entries",
+            "resolve_vds",
         ):
             opt_value = getattr(options, opt_name)
             if opt_value is not None:

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/io/config/tests/test_confighandler.py

@@ -46,6 +46,7 @@ class _ARParseMock(object):
         self.use_abs_path_for_vds = None
         self.open_mode_for_reading = "robust"
         self.output_entries = None
+        self.resolve_vds = None
 
 
 def test_creation_from_config_file(tmp_path):

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/models/h52nx/general_section.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 from typing import Literal
 from collections import deque
 from pydantic import Field, field_serializer, field_validator, ConfigDict
@@ -14,6 +15,15 @@ from nxtomomill.models.utils import (
 from ..base.general_section import GeneralSection as _GeneralSectionBase
 
 
+def _default_resolve_vds() -> bool:
+    """
+    Default value for 'resolve_vds'. Fallback on the 'NXTOMOMILL_RESOLVE_VDS'
+    environment variable when set, else defaults to True.
+    """
+    env_value = os.environ.get("NXTOMOMILL_RESOLVE_VDS", True)
+    return convert_str_to_bool(env_value)
+
+
 class GeneralSection(_GeneralSectionBase):
     model_config = ConfigDict(validate_assignment=True, validate_by_name=True)
 
@@ -69,6 +79,17 @@ class GeneralSection(_GeneralSectionBase):
         default="robust",
         description="How to open the HDF5 file for reading. Either 'robust' mode (disabling file locking) or 'safe'(with file locking)",
     )
+    resolve_vds: bool = Field(
+        default_factory=_default_resolve_vds,
+        description=(
+            "Resolve external links and virtual datasets (VDS) down to their final "
+            "source when building the output NXtomo. Disabling this can speed up "
+            "the conversion for datasets with many nested links, at the cost of "
+            "the output file containing VDS pointing to other VDS instead of "
+            "direct links to the raw data. Defaults to the 'NXTOMOMILL_RESOLVE_VDS' "
+            "environment variable if set, else True."
+        ),
+    )
 
     @property
     def request_input(self) -> bool:
@@ -147,6 +168,7 @@ class GeneralSection(_GeneralSectionBase):
         "create_control_data",
         "mechanical_lr_flip",
         "mechanical_ud_flip",
+        "resolve_vds",
         mode="before",
     )
     @classmethod

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill/models/h52nx/h52nx.py

@@ -57,6 +57,7 @@ class H52nxModel(
                 mechanical_ud_flip=self.mechanical_ud_flip,
                 open_mode_for_reading=self.open_mode_for_reading,
                 output_entries=self.output_entries,
+                resolve_vds=self.resolve_vds,
             ),
             keys_section=KeysSection(
                 valid_camera_names=self.valid_camera_names,

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1/nxtomomill.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.2.0.dev0
+Version: 2.2.0.dev1
 Summary: applications and library to convert raw format to NXtomo format
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: 
@@ -58,7 +58,7 @@ Requires-Dist: silx>=2.0
 Requires-Dist: nxtomo>=3.1.0dev1
 Requires-Dist: pint
 Requires-Dist: packaging
-Requires-Dist: tomoscan[full]>=3.0.0dev0
+Requires-Dist: tomoscan>=3.0.0dev0
 Requires-Dist: tomobase>=0.0.0dev0
 Requires-Dist: tqdm
 Requires-Dist: pydantic

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill.egg-info/SOURCES.txt

@@ -45,7 +45,6 @@ nxtomomill/converter/version.py
 nxtomomill/converter/dxfile/__init__.py
 nxtomomill/converter/dxfile/dxfileconverter.py
 nxtomomill/converter/dxfile/tests/test_dxfile.py
-nxtomomill/converter/edf/_Blosc2Jp2kWrapper.py
 nxtomomill/converter/edf/__init__.py
 nxtomomill/converter/edf/checks.py
 nxtomomill/converter/edf/edfconverter.py

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/nxtomomill.egg-info/requires.txt

@@ -4,7 +4,7 @@ silx>=2.0
 nxtomo>=3.1.0dev1
 pint
 packaging
-tomoscan[full]>=3.0.0dev0
+tomoscan>=3.0.0dev0
 tomobase>=0.0.0dev0
 tqdm
 pydantic

{nxtomomill-2.2.0.dev0 → nxtomomill-2.2.0.dev1}/pyproject.toml

@@ -7,7 +7,7 @@ authors = [
     { name = "Jérôme Lesaint", email = "jerome.lesaint@esrf.fr" },
     { name = "Alessandro Mirone", email = "mirone@esrf.fr" }
 ]
-version = "2.2.0dev0"
+version = "2.2.0dev1"
 description = "applications and library to convert raw format to NXtomo format"
 readme = { file = "README.md", content-type = "text/markdown" }
 
@@ -39,7 +39,7 @@ dependencies = [
     "nxtomo>=3.1.0dev1",
     "pint",
     "packaging",
-    "tomoscan[full] >=3.0.0dev0",
+    "tomoscan>=3.0.0dev0",
     "tomobase>=0.0.0dev0",
     "tqdm",
     "pydantic",