nxtomomill 2.1.0.dev4__tar.gz → 2.1.1__tar.gz

{nxtomomill-2.1.0.dev4/nxtomomill.egg-info → nxtomomill-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.1.0.dev4
+Version: 2.1.1
 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: 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/doc/conf.py

@@ -4,26 +4,16 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
 
 # -- Project information -----------------------------------------------------
+from importlib.metadata import version as get_version
 
 project = "nxtomomill"
 copyright = "2020-2025, ESRF"
 author = "P.-O. Autran, J. Lesaint, A. Mirone, C. Nemoz, P. Paleo, H. Payno, A. Sole, N. Vigano"
 
-# The full version, including alpha/beta/rc tags
-release = "2.0"
-version = release
+release = get_version("nxtomomill")
+version = ".".join(release.split(".")[:2])
 
 
 # -- General configuration ---------------------------------------------------

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/app/fluo2nx.py

@@ -13,7 +13,7 @@ import os
 
 from nxtomomill import utils
 from nxtomomill import converter
-from nxtomomill.io.config.fluoconfig import TomoFluoConfig
+from nxtomomill.models.fluo2nx import Fluo2nxModel
 
 from tqdm import tqdm
 
@@ -75,7 +75,8 @@ def main(argv):
     )
 
     options = parser.parse_args(argv[1:])
-    config = TomoFluoConfig()
+    config = Fluo2nxModel()
+
     if options.config is not None:
         config = config.from_cfg_file(options.config)
 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/app/z_concatenate_scans.py

@@ -230,11 +230,13 @@ def main(argv):
         # step 2: insert single 'empty' frame between the two stages (aka dummy frame)
         invalid_nxt = NXtomo(args.entry_name)
         invalid_nxt.instrument.detector.image_key_control = [ImageKey.INVALID]
-        invalid_nxt.energy = nxt.energy.value
+        invalid_nxt.instrument.beam.incident_energy = (
+            nxt.instrument.beam.incident_energy.value
+        )
         invalid_nxt.control.data = np.ones(1, "f")
         invalid_nxt.sample.rotation_angle = [0.0] * _ureg.degree
-        invalid_nxt.instrument.detector.field_of_view = (
-            nxt.instrument.detector.field_of_view.value
+        invalid_nxt.instrument.detector.half_acquisition = (
+            nxt.instrument.detector.half_acquisition
         )
         invalid_nxt.instrument.detector.x_pixel_size = (
             nxt.instrument.detector.x_pixel_size.value

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/edf/tests/test_edf2nx.py

@@ -14,10 +14,12 @@ from tomoscan import version
 from tomoscan.esrf.mock import MockEDF
 from tomoscan.esrf.scan.edfscan import EDFTomoScan
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
-from tomoscan.esrf.scan.utils import cwd_context, dump_info_file
+from tomoscan.esrf.scan.utils import dump_info_file
 from tomoscan.validator import is_valid_for_reconstruction
 from tomoscan.io import HDF5File, get_swmr_mode
 
+from nxtomo.io import cwd_context
+
 from nxtomomill import converter
 from nxtomomill.converter.edf.checks import OUPUT_CHECK
 from nxtomomill.models.edf2nx import EDF2nxModel

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/fluo/fluoconverter.py

@@ -101,7 +101,7 @@ def from_fluo_to_nx(configuration: Fluo2nxModel, progress: tqdm | None = None) -
                 my_nxtomo.instrument.detector.image_key_control = [
                     ImageKey.PROJECTION
                 ] * elmt_line_data.shape[0]
-                my_nxtomo.sample.rotation_angle = scan.rot_angles_deg * _ureg.degree
+                my_nxtomo.sample.rotation_angle = scan.rot_angles_deg
                 my_nxtomo.instrument.detector.x_pixel_size = scan.pixel_size * _ureg(
                     "m"
                 )
@@ -112,7 +112,7 @@ def from_fluo_to_nx(configuration: Fluo2nxModel, progress: tqdm | None = None) -
                 # define a value to sample-detector and source-sample distance. To be set to the real value in the future
                 my_nxtomo.instrument.detector.distance = 1.0 * _ureg.meter
                 my_nxtomo.instrument.source.distance = 1.0 * _ureg.meter
-                my_nxtomo.energy = scan.energy * _ureg.keV
+                my_nxtomo.instrument.beam.incident_energy = scan.energy * _ureg.keV
 
                 data_path = f"{det}_{element}_{line}"
                 my_nxtomo.save(
@@ -202,7 +202,7 @@ def from_blissfluo_to_nx(
             )
 
             my_nxtomo.instrument.name = configuration.instrument_section.instrument_name
-            my_nxtomo.energy = scan.energy
+            my_nxtomo.instrument.beam.incident_energy = scan.energy
 
             data_path = f"{det}_{line}"
             my_nxtomo.save(

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/fluo/fluoscan.py

@@ -63,6 +63,10 @@ class FluoTomoScanBase:
     def __post_init__(self):
         self.detected_folders = self.detect_folders()
         self.detected_detectors = tuple(self.detect_detectors())
+
+        # Ensure given detectors is a tuple
+        if not isinstance(self.detectors, tuple):
+            self.detectors = (self.detectors,)
         self.get_metadata_from_h5_file()
         _logger.info(f"Detectors: {self.detected_detectors}")
         if len(self.detectors) == 0:
@@ -113,7 +117,7 @@ class FluoTomoScanBase:
         if len(self.detected_folders) == 0:
             raise ValueError("No folder found, unable to load metadata")
         h5_path = os.path.join(self.scan, self.detected_folders[0])
-        h5_files = glob.glob1(h5_path, "*.h5")
+        h5_files = glob.glob("*.h5", root_dir=h5_path)
         if len(h5_files) > 1:
             raise ValueError(
                 "More than one hdf5 file in scan directory. Expect only ONE to pick pixel size."
@@ -150,7 +154,7 @@ class FluoTomoScanBase:
             raise ValueError("No folder found, unable to detect detectors")
         proj_1_dir = os.path.join(self.scan, "fluofit", self.detected_folders[0])
         detected_detectors = []
-        file_names = glob.glob1(proj_1_dir, "IMG_*area_density_ngmm2.tif")
+        file_names = glob.glob("IMG_*area_density_ngmm2.tif", root_dir=proj_1_dir)
         for file in file_names:
             det = file.split("_")[1]
             if det not in detected_detectors:
@@ -167,7 +171,9 @@ class FluoTomoScanBase:
             raise ValueError("No folder found, unable to detect elements")
         proj_1_dir = os.path.join(self.scan, "fluofit", self.detected_folders[0])
         detector = self.detectors[0]
-        file_names = glob.glob1(proj_1_dir, f"IMG_{detector}*area_density_ngmm2.tif")
+        file_names = glob.glob(
+            f"IMG_{detector}*area_density_ngmm2.tif", root_dir=proj_1_dir
+        )
         for file in file_names:
             el_str = file.split("_")[2]
             element, line = el_str.split("-")
@@ -197,8 +203,9 @@ class FluoTomoScan3D(FluoTomoScanBase):
     """Dataset manipulation class."""
 
     def detect_folders(self):
-        fit_folders = glob.glob1(
-            os.path.join(self.scan, "fluofit"), rf"{self.dataset_basename}_projection*"
+        fit_folders = glob.glob(
+            rf"{self.dataset_basename}_projection*",
+            root_dir=os.path.join(self.scan, "fluofit"),
         )
         fit_folders.sort()
         proj_indices = [int(f[-3:]) for f in fit_folders]
@@ -284,7 +291,7 @@ class FluoTomoScan2D(FluoTomoScanBase):
     def get_metadata_from_h5_file(self):
         super().get_metadata_from_h5_file()
         h5_path = os.path.join(self.scan, self.detected_folders[0])
-        h5_files = glob.glob1(h5_path, "*.h5")
+        h5_files = glob.glob("*.h5", root_dir=h5_path)
         if len(h5_files) > 1:
             raise ValueError(
                 "More than one hdf5 file in scan directory. Expect only ONE to pick pixel size."

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/fscan/fscanconverter.py

@@ -136,7 +136,7 @@ def from_fscan_to_nx(
     )
 
     if energy is not None:
-        my_nxtomo.energy = energy  # in keV by default
+        my_nxtomo.instrument.beam.incident_energy = energy  # in keV by default
     if distance is not None:
         my_nxtomo.instrument.detector.distance = distance  # in meter
 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/acquisition/standardacquisition.py

@@ -19,6 +19,7 @@ from nxtomo.nxobject.nxdetector import ImageKey
 from nxtomo.nxobject.utils.concatenate import (
     concatenate_pint_quantities as _concatenate_pint_quantities,
 )
+from nxtomo.io import cwd_context
 
 from .utils._context import (
     update_config_keys_from_tomo_config_context,
@@ -520,9 +521,13 @@ class StandardAcquisition(BaseAcquisition):
         return False
 
     def _preprocess_registered_entry(self, entry_url, type_):
-        with EntryReader(
-            entry_url, open_mode_for_reading=self.configuration.open_mode_for_reading
-        ) as entry:
+        with (
+            cwd_context(entry_url.file_path()),
+            EntryReader(
+                entry_url,
+                open_mode_for_reading=self.configuration.open_mode_for_reading,
+            ) as entry,
+        ):
             entry_path = self._entries_o_path[entry_url.path()]
             input_file_path = entry_url.file_path()
             input_file_path = abspath(os.path.relpath(input_file_path, os.getcwd()))
@@ -1293,8 +1298,7 @@ class StandardAcquisition(BaseAcquisition):
             energy = None
 
         if energy is not None:
-            # TODO: better management of energy ? might be energy.beam or energy.instrument.beam ?
-            nx_tomo.energy = energy
+            nx_tomo.instrument.beam.incident_energy = energy
 
         # 3. define instrument
         nx_tomo.instrument.name = self._get_instrument_name()
@@ -1389,9 +1393,10 @@ class StandardAcquisition(BaseAcquisition):
         # Note: default value is False and not None. So if the half_acquisition is not found in the metadata we will set it to False
         nx_tomo.instrument.detector.half_acquisition = half_acquisition
         # fov (deprecated. half-acquisition is preferred)
-        fov = self._get_field_of_view()
-        if fov is not None:
-            nx_tomo.instrument.detector.field_of_view = fov
+        if half_acquisition is None:
+            fov = self._get_field_of_view()
+            if fov is not None:
+                nx_tomo.instrument.detector.field_of_view = fov
 
         # x_rotation_axis_pixel_position
         # TODO Missing calibration mechanism from Bliss

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/acquisition/tests/test_back_and_forth.py

@@ -102,7 +102,7 @@ def test_back_and_forth_conversion(tmp_path):
 
         assert nx_tomo.instrument.detector.distance == 3500 * _ureg.millimeter
         # check energy
-        assert nx_tomo.energy == 10.0 * _ureg.keV
+        assert nx_tomo.instrument.beam.incident_energy == 10.0 * _ureg.keV
         # check sample
         assert nx_tomo.sample.x_pixel_size == 2.4 * _ureg.micrometer
         assert nx_tomo.sample.y_pixel_size == 2.4 * _ureg.micrometer

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/acquisition/tests/test_holotomo.py

@@ -109,7 +109,7 @@ def test_holotomo_conversion_id16a(tmp_path):
         nx_tomo.instrument.detector.distance, 1206.69 * _ureg.millimeter
     )
     # check energy
-    assert nx_tomo.energy == 17.1 * _ureg.keV
+    assert nx_tomo.instrument.beam.incident_energy == 17.1 * _ureg.keV
     # check sample
     numpy.testing.assert_almost_equal(
         nx_tomo.sample.x_pixel_size.magnitude,
@@ -230,7 +230,7 @@ def test_holotomo_conversion_id16b(tmp_path):
         nx_tomo.instrument.detector.distance, 723.908 * _ureg.millimeter
     )
     # check energy
-    assert nx_tomo.energy == 29.6 * _ureg.keV
+    assert nx_tomo.instrument.beam.incident_energy == 29.6 * _ureg.keV
     # check sample
     numpy.testing.assert_almost_equal(
         nx_tomo.sample.x_pixel_size.magnitude,

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/acquisition/tests/test_legacy.py

@@ -51,7 +51,7 @@ def test_S59_68p41b_16mm_6p5mm_F8_0001_dataset(
 
     nxtomo = NXtomo().load(*result[0])
 
-    nxtomo.energy = 70.0 * _ureg.keV
+    nxtomo.instrument.beam.incident_energy = 70.0 * _ureg.keV
     n_frames = 10252
 
     assert len(nxtomo.sample.x_translation) == n_frames
@@ -119,7 +119,7 @@ def test_WGN_01_0000_P_110_8128_D_129(WGN_01_0000_P_110_8128_D_129_Dataset, tmp_
 
     nxtomo = NXtomo().load(*result[0])
 
-    nxtomo.energy = 80.0 * _ureg.keV
+    nxtomo.instrument.beam.incident_energy = 80.0 * _ureg.keV
     n_frames = 4602
 
     assert len(nxtomo.sample.x_translation) == n_frames

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/acquisitionConstructor.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 import os
 import h5py
-import numpy
 import logging
 from tqdm import tqdm
 
@@ -381,7 +380,7 @@ class _AcquisitionConstructorFromTitles(_AcquisitionConstructorBase):
                     return self.sort_fct(name, h5d=h5d)
 
                 groups.sort(key=sort)
-            except numpy.core._exceptions._UFuncNoLoopError:
+            except TypeError:
                 raise ValueError(
                     "Fail to order according to 'start_time'. Probably not all scans have a 'start_time' dataset"
                 )

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/converter/hdf5/tests/test_hdf5converter.py

@@ -9,7 +9,7 @@ import numpy
 import pint
 import shutil
 
-from tomoscan.esrf.scan.utils import cwd_context
+from nxtomo.io import cwd_context
 
 from nxtomomill import converter
 from nxtomomill.tests.datasets import GitlabDataset
@@ -760,7 +760,7 @@ def test_dataset_2(tmp_path):
     config.y_sample_pixel_size_m = 2.7 * 10e-6
 
     config.overwrite = True
-    config.field_of_view = "Half"
+    config.half_acquisition = True
 
     init_url_1 = DataUrl(file_path=file_1, data_path="/1.1", scheme="silx")
 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/utils/utils.py

@@ -13,10 +13,10 @@ from silx.io.url import DataUrl
 from silx.io.utils import get_data
 from silx.utils.deprecation import deprecated
 from silx.utils.enum import Enum as _Enum
-from tomoscan.esrf.scan.utils import cwd_context
 from tomoscan.io import HDF5File
 from nxtomomill.utils.hdf5 import open_hdf5_readonly
 
+from nxtomo.io import cwd_context
 from nxtomo.nxobject.nxdetector import ImageKey
 from nxtomo.utils.frameappender import FrameAppender
 from nxtomo.application.nxtomo import NXtomo
@@ -445,7 +445,7 @@ def str_datetime_to_numpy_datetime64(my_datetime: str | datetime) -> numpy.datet
         )
 
     datetime_as_utc_datetime = datetime_as_datetime.astimezone(timezone.utc)
-    tz_free_datetime_as_datetime = datetime_as_utc_datetime.replace(tzinfo=timezone.utc)
+    tz_free_datetime_as_datetime = datetime_as_utc_datetime.replace(tzinfo=None)
     return numpy.datetime64(tz_free_datetime_as_datetime).astype("<M8[ms]")
 
 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1}/nxtomomill/version.py

@@ -55,9 +55,9 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 2
 MINOR = 1
-MICRO = 0
-RELEV = "dev"  # <16
-SERIAL = 4  # <16
+MICRO = 1
+RELEV = "final"  # <16
+SERIAL = 0  # <16
 
 date = __date__
 

{nxtomomill-2.1.0.dev4 → nxtomomill-2.1.1/nxtomomill.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nxtomomill
-Version: 2.1.0.dev4
+Version: 2.1.1
 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: