nabu 2025.1.0.dev14__py3-none-any.whl → 2025.1.0rc1__py3-none-any.whl

nabu/stitching/stitcher/pre_processing.py

@@ -2,6 +2,7 @@ import numpy
 import logging
 import h5py
 import os
+import pint
 from collections.abc import Iterable
 from silx.io.url import DataUrl
 from silx.io.utils import get_data
@@ -26,8 +27,8 @@ from nabu.stitching.config import (
 from nabu.stitching.utils import find_projections_relative_shifts
 from functools import lru_cache as cache
 from .single_axis import SingleAxisStitcher
-from pyunitsystem.metricsystem import MetricSystem
 
+_ureg = pint.get_application_registry()
 
 _logger = logging.getLogger(__name__)
 
@@ -238,18 +239,18 @@ class PreProcessingStitching(SingleAxisStitcher):
             if not scan_0.field_of_view == scan_1.field_of_view:
                 raise ValueError(f"{scan_0} and {scan_1} have different field of view")
             # check distance
-            if scan_0.distance is None:
+            if scan_0.sample_detector_distance is None:
                 _logger.warning(f"no distance found for {scan_0}")
-            elif not numpy.isclose(scan_0.distance, scan_1.distance, rtol=10e-3):
+            elif not numpy.isclose(scan_0.sample_detector_distance, scan_1.sample_detector_distance, rtol=10e-3):
                 raise ValueError(f"{scan_0} and {scan_1} have different sample / detector distance")
             # check pixel size
-            if not numpy.isclose(scan_0.x_pixel_size, scan_1.x_pixel_size):
+            if not numpy.isclose(scan_0.sample_x_pixel_size, scan_1.sample_x_pixel_size):
                 raise ValueError(
-                    f"{scan_0} and {scan_1} have different x pixel size. {scan_0.x_pixel_size} vs {scan_1.x_pixel_size}"
+                    f"{scan_0} and {scan_1} have different x pixel size. {scan_0.sample_x_pixel_size} vs {scan_1.sample_x_pixel_size}"
                 )
-            if not numpy.isclose(scan_0.y_pixel_size, scan_1.y_pixel_size):
+            if not numpy.isclose(scan_0.sample_y_pixel_size, scan_1.sample_y_pixel_size):
                 raise ValueError(
-                    f"{scan_0} and {scan_1} have different y pixel size. {scan_0.y_pixel_size} vs {scan_1.y_pixel_size}"
+                    f"{scan_0} and {scan_1} have different y pixel size. {scan_0.sample_y_pixel_size} vs {scan_1.sample_y_pixel_size}"
                 )
 
         for scan in self.series:
@@ -291,7 +292,7 @@ class PreProcessingStitching(SingleAxisStitcher):
                 axis_N_pos_px = []
                 for scan, pos_in_mm in zip(self.series, pos_as_mm):
                     pixel_size_m = self.configuration.pixel_size or scan.pixel_size
-                    axis_N_pos_px.append((pos_in_mm / MetricSystem.MILLIMETER.value) / pixel_size_m)
+                    axis_N_pos_px.append((pos_in_mm * _ureg.millimeter).to_base_units().magnitude / pixel_size_m)
                 return axis_N_pos_px
             else:
                 # deduce from motor position and pixel size
@@ -471,7 +472,7 @@ class PreProcessingStitching(SingleAxisStitcher):
         """
         nx_tomo = NXtomo()
 
-        nx_tomo.energy = self.series[0].energy
+        nx_tomo.energy = self.series[0].energy * _ureg.keV
         start_times = list(filter(None, [scan.start_time for scan in self.series]))
         end_times = list(filter(None, [scan.end_time for scan in self.series]))
 
@@ -495,9 +496,9 @@ class PreProcessingStitching(SingleAxisStitcher):
 
         # handle detector (without frames)
         nx_tomo.instrument.detector.field_of_view = self.series[0].field_of_view
-        nx_tomo.instrument.detector.distance = self.series[0].distance
-        nx_tomo.instrument.detector.x_pixel_size = self.series[0].x_pixel_size
-        nx_tomo.instrument.detector.y_pixel_size = self.series[0].y_pixel_size
+        nx_tomo.instrument.detector.distance = self.series[0].sample_detector_distance * _ureg.meter
+        nx_tomo.instrument.detector.x_pixel_size = self.series[0].x_pixel_size * _ureg.meter
+        nx_tomo.instrument.detector.y_pixel_size = self.series[0].y_pixel_size * _ureg.meter
         nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
         nx_tomo.instrument.detector.tomo_n = n_proj
         # note: stitching process insure un-flipping of frames. So make sure transformations is defined as an empty set
@@ -505,13 +506,13 @@ class PreProcessingStitching(SingleAxisStitcher):
 
         if isinstance(self.series[0], NXtomoScan):
             # note: first scan is always the reference as order to read data (so no rotation_angle inversion here)
-            rotation_angle = numpy.asarray(self.series[0].rotation_angle)
+            rotation_angle = numpy.asarray(self.series[0].rotation_angle) * _ureg.degree
             nx_tomo.sample.rotation_angle = rotation_angle[
                 numpy.asarray(self.series[0].image_key_control) == ImageKey.PROJECTION.value
             ]
         elif isinstance(self.series[0], EDFTomoScan):
-            nx_tomo.sample.rotation_angle = numpy.linspace(
-                start=0, stop=self.series[0].scan_range, num=self.series[0].tomo_n
+            nx_tomo.sample.rotation_angle = (
+                numpy.linspace(start=0, stop=self.series[0].scan_range, num=self.series[0].tomo_n) * _ureg.degree
             )
         else:
             raise NotImplementedError(
@@ -529,8 +530,11 @@ class PreProcessingStitching(SingleAxisStitcher):
             else:
                 raise RuntimeError("slices must be instance of a slice or of an iterable")  # noqa: TRY004
 
-        nx_tomo.sample.rotation_angle = apply_slices_selection(
-            array=nx_tomo.sample.rotation_angle, slices=self._slices_to_stitch
+        nx_tomo.sample.rotation_angle = (
+            apply_slices_selection(
+                array=nx_tomo.sample.rotation_angle.to_base_units().magnitude, slices=self._slices_to_stitch
+            )
+            * _ureg.degree
         )
 
         # handle sample
@@ -559,7 +563,7 @@ class PreProcessingStitching(SingleAxisStitcher):
                 # note: if at least one has missing values the numpy.Array(x_translation) with create an error as well
                 x_translation = [0.0] * n_proj
                 _logger.warning("Unable to fin input nxtomo x_translation values. Set it to 0.0")
-            nx_tomo.sample.x_translation = x_translation
+            nx_tomo.sample.x_translation = x_translation * _ureg.meter
 
             y_translation = [
                 get_sample_translation_for_projs(scan, "y_translation")
@@ -574,7 +578,7 @@ class PreProcessingStitching(SingleAxisStitcher):
             else:
                 y_translation = [0.0] * n_proj
                 _logger.warning("Unable to fin input nxtomo y_translation values. Set it to 0.0")
-            nx_tomo.sample.y_translation = y_translation
+            nx_tomo.sample.y_translation = y_translation * _ureg.meter
             z_translation = [
                 get_sample_translation_for_projs(scan, "z_translation")
                 for scan in self.series
@@ -588,7 +592,7 @@ class PreProcessingStitching(SingleAxisStitcher):
             else:
                 z_translation = [0.0] * n_proj
                 _logger.warning("Unable to fin input nxtomo z_translation values. Set it to 0.0")
-            nx_tomo.sample.z_translation = z_translation
+            nx_tomo.sample.z_translation = z_translation * _ureg.meter
 
             nx_tomo.sample.name = self.series[0].sample_name
 

nabu/stitching/tests/test_config.py

@@ -10,7 +10,7 @@ from nabu.stitching.overlap import OverlapStitchingStrategy
 from nabu.stitching import config as stiching_config
 
 
-_stitching_types = list(stiching_config.StitchingType.values())
+_stitching_types = [st.value for st in list(stiching_config.StitchingType)]
 _stitching_types.append(None)
 
 
@@ -37,7 +37,7 @@ def test_stitching_config(stitching_type, option_level):
 
         assert "stitching" in config
         assert "type" in config["stitching"]
-        stitching_type = stiching_config.StitchingType.from_value(config["stitching"]["type"])
+        stitching_type = stiching_config.StitchingType(config["stitching"]["type"])
         if stitching_type is stiching_config.StitchingType.Z_POSTPROC:
             assert isinstance(
                 stiching_config.dict_to_config_obj(config),
@@ -82,7 +82,7 @@ def test_stitching_config(stitching_type, option_level):
         assert isinstance(config_class_instance.to_dict(), dict)
 
 
-@pytest.mark.parametrize("stitching_strategy", OverlapStitchingStrategy.values())
+@pytest.mark.parametrize("stitching_strategy", [oss for oss in OverlapStitchingStrategy])
 @pytest.mark.parametrize("overwrite_results", (True, "False", 0, "1"))
 @pytest.mark.parametrize(
     "axis_shifts",

nabu/stitching/tests/test_y_preprocessing_stitching.py

@@ -1,6 +1,7 @@
 import os
 import pytest
 import numpy
+import pint
 from tqdm import tqdm
 
 from nabu.stitching.y_stitching import y_stitching
@@ -9,6 +10,8 @@ from nxtomo.application.nxtomo import NXtomo
 from nxtomo.nxobject.nxdetector import ImageKey
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
 
+_ureg = pint.UnitRegistry()
+
 
 def build_nxtomos(output_dir, flip_lr, flip_ud) -> tuple:
     r"""
@@ -52,10 +55,10 @@ def build_nxtomos(output_dir, flip_lr, flip_ud) -> tuple:
 
         n_projs = 3
         nx_tomo = NXtomo()
-        nx_tomo.sample.x_translation = [0] * (n_projs + 2)
-        nx_tomo.sample.y_translation = [frame_y_position] * (n_projs + 2)
-        nx_tomo.sample.z_translation = [0] * (n_projs + 2)
-        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=(n_projs + 2), endpoint=False)
+        nx_tomo.sample.x_translation = ([0] * (n_projs + 2)) * _ureg.meter
+        nx_tomo.sample.y_translation = ([frame_y_position] * (n_projs + 2)) * _ureg.meter
+        nx_tomo.sample.z_translation = ([0] * (n_projs + 2)) * _ureg.meter
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=(n_projs + 2), endpoint=False) * _ureg.degree
         nx_tomo.instrument.detector.image_key_control = (
             ImageKey.DARK_FIELD,
             ImageKey.FLAT_FIELD,
@@ -63,10 +66,10 @@ def build_nxtomos(output_dir, flip_lr, flip_ud) -> tuple:
             ImageKey.PROJECTION,
             ImageKey.PROJECTION,
         )
-        nx_tomo.instrument.detector.x_pixel_size = 1.0
-        nx_tomo.instrument.detector.y_pixel_size = 1.0
-        nx_tomo.instrument.detector.distance = 2.3
-        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.x_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.y_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.distance = 2.3 * _ureg.meter
+        nx_tomo.energy = 19.2 * _ureg.keV
         nx_tomo.instrument.detector.data = numpy.stack(
             (
                 my_dark_data,

nabu/stitching/tests/test_z_postprocessing_stitching.py

@@ -395,7 +395,7 @@ def test_vol_z_stitching_with_alignment_axis_2(tmp_path, alignment_axis_2):
         axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
         slice_for_cross_correlation="middle",
         voxel_size=None,
-        alignment_axis_2=AlignmentAxis2.from_value(alignment_axis_2),
+        alignment_axis_2=AlignmentAxis2(alignment_axis_2),
     )
 
     stitcher = PostProcessZStitcher(z_stich_config, progress=None)
@@ -512,7 +512,7 @@ def test_vol_z_stitching_with_alignment_axis_1(tmp_path, alignment_axis_1):
         axis_2_params={"img_reg_method": ShiftAlgorithm.NONE},
         slice_for_cross_correlation="middle",
         voxel_size=None,
-        alignment_axis_1=AlignmentAxis1.from_value(alignment_axis_1),
+        alignment_axis_1=AlignmentAxis1(alignment_axis_1),
     )
 
     stitcher = PostProcessZStitcher(z_stich_config, progress=None)

nabu/stitching/tests/test_z_preprocessing_stitching.py

@@ -1,4 +1,5 @@
 import os
+import pint
 from silx.image.phantomgenerator import PhantomGenerator
 from scipy.ndimage import shift as scipy_shift
 import numpy
@@ -17,6 +18,8 @@ from tomoscan.esrf.scan.nxtomoscan import NXtomoScan
 from nabu.stitching.utils import ShiftAlgorithm
 import h5py
 
+_ureg = pint.get_application_registry()
+
 
 _stitching_configurations = (
     # simple case where shifts are provided
@@ -82,13 +85,13 @@ def test_PreProcessZStitcher(tmp_path, dtype, configuration):
     scans = []
     for (i_frame, frame), z_pos in zip(enumerate(frames), z_position):
         nx_tomo = NXtomo()
-        nx_tomo.sample.z_translation = [z_pos] * n_proj
-        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False)
+        nx_tomo.sample.z_translation = ([z_pos] * n_proj) * _ureg.meter
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False) * _ureg.degree
         nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
-        nx_tomo.instrument.detector.x_pixel_size = 1.0
-        nx_tomo.instrument.detector.y_pixel_size = 1.0
-        nx_tomo.instrument.detector.distance = 2.3
-        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.x_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.y_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.distance = 2.3 * _ureg.meter
+        nx_tomo.energy = 19.2 * _ureg.keV
         nx_tomo.instrument.detector.data = numpy.asarray([frame] * n_proj)
 
         file_path = os.path.join(raw_data_dir, f"nxtomo_{i_frame}.nx")
@@ -160,8 +163,8 @@ def test_PreProcessZStitcher(tmp_path, dtype, configuration):
         )
 
     # check also other metadata are here
-    assert created_nx_tomo.instrument.detector.distance.value == 2.3
-    assert created_nx_tomo.energy.value == 19.2
+    assert created_nx_tomo.instrument.detector.distance == 2.3 * _ureg.meter
+    assert created_nx_tomo.energy == 19.2 * _ureg.keV
     numpy.testing.assert_array_equal(
         created_nx_tomo.instrument.detector.image_key_control,
         numpy.asarray([ImageKey.PROJECTION.PROJECTION] * n_proj),
@@ -228,13 +231,13 @@ def build_nxtomos(output_dir) -> tuple:
     scans = []
     for (i_frame, frame), z_pos in zip(enumerate(frames), z_positions):
         nx_tomo = NXtomo()
-        nx_tomo.sample.z_translation = [z_pos] * n_projs
-        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_projs, endpoint=False)
+        nx_tomo.sample.z_translation = [z_pos] * n_projs * _ureg.meter
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_projs, endpoint=False) * _ureg.degree
         nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_projs
-        nx_tomo.instrument.detector.x_pixel_size = 1.0
-        nx_tomo.instrument.detector.y_pixel_size = 1.0
-        nx_tomo.instrument.detector.distance = 2.3
-        nx_tomo.energy = 19.2
+        nx_tomo.instrument.detector.x_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.y_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.distance = 2.3 * _ureg.meter
+        nx_tomo.energy = 19.2 * _ureg.keV
         nx_tomo.instrument.detector.data = frame
 
         file_path = os.path.join(output_dir, f"nxtomo_{i_frame}.nx")
@@ -373,15 +376,15 @@ def test_frame_flip(tmp_path):
     scans = []
     for (i_frame, frame), z_pos, x_flip, y_flip in zip(enumerate(frames), z_position, x_flips, y_flips):
         nx_tomo = NXtomo()
-        nx_tomo.sample.z_translation = [z_pos] * n_proj
-        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False)
+        nx_tomo.sample.z_translation = [z_pos] * n_proj * _ureg.meter
+        nx_tomo.sample.rotation_angle = numpy.linspace(0, 180, num=n_proj, endpoint=False) * _ureg.degree
         nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
-        nx_tomo.instrument.detector.x_pixel_size = 1.0
-        nx_tomo.instrument.detector.y_pixel_size = 1.0
-        nx_tomo.instrument.detector.distance = 2.3
+        nx_tomo.instrument.detector.x_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.y_pixel_size = 1.0 * _ureg.meter
+        nx_tomo.instrument.detector.distance = 2.3 * _ureg.meter
         nx_tomo.instrument.detector.transformations.add_transformation(DetZFlipTransformation(flip=x_flip))
         nx_tomo.instrument.detector.transformations.add_transformation(DetYFlipTransformation(flip=y_flip))
-        nx_tomo.energy = 19.2
+        nx_tomo.energy = 19.2 * _ureg.keV
         nx_tomo.instrument.detector.data = numpy.asarray([frame] * n_proj)
 
         file_path = os.path.join(raw_data_dir, f"nxtomo_{i_frame}.nx")

nabu/stitching/utils/utils.py

@@ -1,3 +1,4 @@
+from enum import Enum
 from packaging.version import parse as parse_version
 from typing import Optional, Union
 import logging
@@ -6,7 +7,6 @@ import numpy
 from tomoscan.scanbase import TomoScanBase
 from tomoscan.volumebase import VolumeBase
 from nxtomo.utils.transformation import build_matrix, DetYFlipTransformation
-from silx.utils.enum import Enum as _Enum
 from scipy.fft import rfftn as local_fftn
 from scipy.fft import irfftn as local_ifftn
 from ..alignment import AlignmentAxis1, AlignmentAxis2, PaddedRawData
@@ -36,7 +36,7 @@ else:
     __has_sk_phase_correlation__ = True
 
 
-class ShiftAlgorithm(_Enum):
+class ShiftAlgorithm(Enum):
     """All generic shift search algorithm"""
 
     NABU_FFT = "nabu-fft"
@@ -58,7 +58,7 @@ class ShiftAlgorithm(_Enum):
         if value in ("", None):
             return ShiftAlgorithm.NONE
         else:
-            return super().from_value(value=value)
+            return super().__new__(cls, value)
 
 
 def find_frame_relative_shifts(
@@ -72,7 +72,7 @@ def find_frame_relative_shifts(
     y_shifts_params: Optional[dict] = None,
 ):
     """
-    :param overlap_axis: axis in [0, 1] on which the overlap exists. In image space. So 0 is aka y and 1 as x
+    :param overlap_axis: axis in [0, 1] on which the overlap exists. In image space. So 0 is aka y and 1 as x.
     """
     if overlap_axis not in (0, 1):
         raise ValueError(f"overlap_axis should be in (0, 1). Get {overlap_axis}")
@@ -199,8 +199,8 @@ def find_volumes_relative_shifts(
     else:
         raise ValueError(f"Stitching is done in 3D space. Expect axis to be in [0,2]. Get {overlap_axis}")
 
-    alignment_axis_2 = AlignmentAxis2.from_value(alignment_axis_2)
-    alignment_axis_1 = AlignmentAxis1.from_value(alignment_axis_1)
+    alignment_axis_2 = AlignmentAxis2(alignment_axis_2)
+    alignment_axis_1 = AlignmentAxis1(alignment_axis_1)
     assert dim_axis_1 > 0, "dim_axis_1 <= 0"
 
     if isinstance(slice_for_shift, str):
@@ -500,7 +500,7 @@ def find_shift_correlate(img1, img2, padding_mode="reflect"):
         padding_mode,
     )
 
-    img_shape = img1.shape[-2:]
+    img_shape = cc.shape  # Because cc.shape can differ from img_2.shape (e.g. in case of odd nb of cols)
     cc_vs = numpy.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
     cc_hs = numpy.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
 

nabu/testutils.py

@@ -41,10 +41,7 @@ def generate_tests_scenarios(configurations):
       - the key is the name of a parameter
       - the value is one value of this parameter
     """
-    scenarios = [
-        {key: val for key, val in zip(configurations.keys(), p_)}  # noqa: C416
-        for p_ in product(*configurations.values())
-    ]
+    scenarios = [{key: val for key, val in zip(configurations.keys(), p_)} for p_ in product(*configurations.values())]
     return scenarios
 
 

nabu/utils.py

@@ -1,3 +1,4 @@
+from bisect import bisect_left
 from fnmatch import fnmatch
 from functools import partial
 import os
@@ -538,6 +539,18 @@ def restore_items_in_list(list_, removed_items):
         list_.insert(idx, val)
 
 
+def search_sorted(arr, val):
+    """
+    Binary search that returns the "nearest" index given a query,
+    i.e find "i" that minimizes   abs(arr[i] - val)
+    It does not return the "insersion point" contrarily to numpy.searchsorted() or bisect_left
+    """
+    pos = bisect_left(arr, val)
+    if pos == len(arr):
+        return len(arr) - 1
+    return pos - 1 if abs(val - arr[pos - 1]) < abs(arr[pos] - val) else pos
+
+
 def check_supported(param_value, available, param_desc):
     if param_value not in available:
         raise ValueError("Unsupported %s '%s'. Available are: %s" % (param_desc, param_value, str(available)))

{nabu-2025.1.0.dev14.dist-info → nabu-2025.1.0rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0.dev14
+Version: 2025.1.0rc1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>
@@ -14,7 +14,6 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -26,14 +25,14 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py>=3.0
 Requires-Dist: silx>=0.15.0
-Requires-Dist: tomoscan>=2.1.5
+Requires-Dist: tomoscan>=2.2.0a5
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile