nabu 2025.1.0rc5__tar.gz → 2025.1.1__tar.gz

{nabu-2025.1.0rc5/nabu.egg-info → nabu-2025.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc5
+Version: 2025.1.1
 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>

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2025.1.0-rc5"
+__version__ = "2025.1.1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/estimation/motion.py

@@ -1,5 +1,6 @@
 from enum import Enum
 from multiprocessing.pool import ThreadPool
+from warnings import warn
 import numpy as np
 from ..utils import get_num_threads
 
@@ -218,12 +219,18 @@ class MotionEstimation:
             return _normalize_with_reference(a_all[-n_outward_projs:])
 
     def _configure_shifts_estimator(self, shifts_estimator, shifts_estimator_kwargs):
-        self.shifts_estimator = shifts_estimator
         if shifts_estimator not in self._shifts_estimators_default_kwargs:
             raise NotImplementedError(
                 f"Unknown estimator shifts '{shifts_estimator}', available are {list(self._shifts_estimators_default_kwargs.keys())}"
             )
-        self._shifts_estimator_kwargs = self._shifts_estimators_default_kwargs[shifts_estimator].copy()
+        self.shifts_estimator = shifts_estimator
+        if self.shifts_estimator == "phase_cross_correlation" and phase_cross_correlation is None:
+            warn(
+                "shift estimator was set to 'phase_cross_correlation' but it requires scikit-image which is not available. Falling back to 'DetectorTranslationAlongBeam'",
+                Warning,
+            )
+            self.shifts_estimator = "DetectorTranslationAlongBeam"
+        self._shifts_estimator_kwargs = self._shifts_estimators_default_kwargs[self.shifts_estimator].copy()
         self._shifts_estimator_kwargs.update(shifts_estimator_kwargs or {})
 
     def _find_shifts(self, img1, img2):

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/io/cast_volume.py

@@ -142,7 +142,7 @@ def cast_volume(
     remove_input_volume: bool = False,
 ) -> VolumeBase:
     """
-    cast givent volume to output_volume of 'output_data_type' type
+    cast given volume to output_volume of 'output_data_type' type
 
     :param VolumeBase input_volume:
     :param VolumeBase output_volume:
@@ -231,6 +231,7 @@ def cast_volume(
                 data_max=data_max,
                 rescale_min_percentile=rescale_min_percentile,
                 rescale_max_percentile=rescale_max_percentile,
+                default_value_for_nan=new_min,
             ).astype(output_data_type)
         else:
             output_slice = input_slice.astype(output_data_type)
@@ -268,25 +269,46 @@ def clamp_and_rescale_data(
     data_max=None,
     rescale_min_percentile=RESCALE_MIN_PERCENTILE,
     rescale_max_percentile=RESCALE_MAX_PERCENTILE,
+    default_value_for_nan=None,
+    do_float64=True,
 ):
     """
     rescale data to 'new_min', 'new_max'
 
-    :param numpy.ndarray data: data to be rescaled
-    :param dtype output_dtype: output dtype
-    :param new_min: rescaled data new min (clamp min value)
-    :param new_max: rescaled data new max (clamp max value)
-    :param data_min: `data` min value to clamp to new_min. Any lower value will also be clamp to new_min.
-    :param data_max: `data` max value to clamp to new_max. Any hight value will also be clamp to new_max.
-    :param rescale_min_percentile: if `data_min` is None will set data_min to 'rescale_min_percentile'
-    :param rescale_max_percentile: if `data_max` is None will set data_min to 'rescale_max_percentile'
+    Parameters
+    ----------
+    data: numpy.ndarray
+        Data to be rescaled (image or volume)
+    new_min: scalar
+        Rescaled data new min (clamp min value)
+    new_max: scalar
+        Rescaled data new min (clamp max value)
+    data_min: scalar, optional
+        Data minimum value. If not provided, will re-compute the min() over data.
+    data_max: scalar, optional
+        Data maximum value. If not provided, will re-compute the min() over data.
+    rescale_min_percentile: scalar, optional
+        if `data_min` is None will set data_min to 'rescale_min_percentile'
+    rescale_max_percentile
+        if `data_max` is None will set data_min to 'rescale_max_percentile'
+    default_value_for_nan: scalar, optional
+        Value that will replace NaNs, if any. Default is None (keep NaNs, will likely raise an error)
+    do_float64
+        Whether to do internal computations in float64. Recommended when casting from float32 to int32 for example.
     """
+    if do_float64 and data.dtype.itemsize < 8:
+        data = numpy.float64(data)
     if data_min is None:
-        data_min = numpy.percentile(data, rescale_min_percentile)
+        data_min = numpy.nanpercentile(data, rescale_min_percentile)
     if data_max is None:
-        data_max = numpy.percentile(data, rescale_max_percentile)
+        data_max = numpy.nanpercentile(data, rescale_max_percentile)
     # rescale data
     rescaled_data = rescale_data(data, new_min=new_min, new_max=new_max, data_min=data_min, data_max=data_max)
+    # Handle NaNs
+    if default_value_for_nan is not None:
+        isnan_mask = numpy.isnan(rescaled_data)
+        if numpy.any(isnan_mask):
+            rescaled_data[isnan_mask] = default_value_for_nan
     # clamp data
     rescaled_data[rescaled_data < new_min] = new_min
     rescaled_data[rescaled_data > new_max] = new_max

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/io/reader.py

@@ -556,7 +556,11 @@ class VolReaderBase:
             slice_x = None
         if isinstance(sub_region, (tuple, list)):
             slice_angle, slice_z, slice_x = sub_region
-        self.sub_region = (slice_angle or slice(None, None), slice_z or slice(None, None), slice_x or slice(None, None))
+        self.sub_region = (
+            slice_angle if slice_angle is not None else slice(None, None),
+            slice_z if slice_z is not None else slice(None, None),
+            slice_x if slice_x is not None else slice(None, None),
+        )
 
     def _set_processing_function(self, processing_func, processing_func_args, processing_func_kwargs):
         self.processing_func = processing_func
@@ -682,9 +686,13 @@ class NXTomoReader(VolReaderBase):
             # In this case, we can use h5py read_direct() to avoid extraneous memory consumption
             image_key_slice = self._image_key_slices[0]
             # merge image key selection and user selection (if any)
-            self._source_selection = (
-                merge_slices(image_key_slice, self.sub_region[0] or slice(None, None)),
-            ) + self.sub_region[1:]
+            angles_slice = self.sub_region[0]
+            if isinstance(angles_slice, slice) or angles_slice is None:
+                angles_slice = merge_slices(image_key_slice, self.sub_region[0] or slice(None, None))
+            else:  # assuming numpy array
+                # TODO more elegant
+                angles_slice = np.arange(self.data_shape_total[0], dtype=np.uint64)[image_key_slice][angles_slice]
+            self._source_selection = (angles_slice,) + self.sub_region[1:]
         else:
             user_selection_dim0 = self.sub_region[0]
             indices = np.arange(self.data_shape_total[0])

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/io/tests/test_readers.py

@@ -1,41 +1,23 @@
 from math import ceil
 from tempfile import TemporaryDirectory
-from dataclasses import dataclass
 from tomoscan.io import HDF5File
 import pytest
 import numpy as np
 from nxtomo.application.nxtomo import ImageKey
 from tomoscan.esrf import EDFVolume
 from nabu.pipeline.reader import NXTomoReaderBinning
-from nabu.testutils import utilstest, __do_long_tests__, get_file
+from nabu.testutils import utilstest, __do_long_tests__, get_file, get_dummy_nxtomo_info
 from nabu.utils import indices_to_slices, merge_slices
 from nabu.io.reader import EDFStackReader, NXTomoReader, NXDarksFlats
-
-
-@dataclass
-class SimpleNXTomoDescription:
-    n_darks: int = 0
-    n_flats1: int = 0
-    n_projs: int = 0
-    n_flats2: int = 0
-    n_align: int = 0
-    frame_shape: tuple = None
-    dtype: np.dtype = np.uint16
+from nabu.resources.dataset_analyzer import analyze_dataset
 
 
 @pytest.fixture(scope="class")
 def bootstrap_nx_reader(request):
     cls = request.cls
-
-    cls.nx_fname = utilstest.getfile("dummy_nxtomo.nx")
-    cls.nx_data_path = "entry/instrument/detector/data"
-    cls.data_desc = SimpleNXTomoDescription(
-        n_darks=10, n_flats1=11, n_projs=100, n_flats2=11, n_align=12, frame_shape=(11, 10), dtype=np.uint16
+    cls.nx_fname, cls.data_desc, cls.image_key, cls.projs_vals, cls.darks_vals, cls.flats1_vals, cls.flats2_vals = (
+        get_dummy_nxtomo_info()
     )
-    cls.projs_vals = np.arange(cls.data_desc.n_projs) + cls.data_desc.n_flats1 + cls.data_desc.n_darks
-    cls.darks_vals = np.arange(cls.data_desc.n_darks)
-    cls.flats1_vals = np.arange(cls.data_desc.n_darks, cls.data_desc.n_darks + cls.data_desc.n_flats1)
-    cls.flats2_vals = np.arange(cls.data_desc.n_darks, cls.data_desc.n_darks + cls.data_desc.n_flats2)
 
     yield
     # teardown
@@ -45,7 +27,7 @@ def bootstrap_nx_reader(request):
 class TestNXReader:
     def test_incorrect_path(self):
         with pytest.raises(FileNotFoundError):
-            reader = NXTomoReader("/invalid/path", self.nx_data_path)
+            reader = NXTomoReader("/invalid/path")
         with pytest.raises(KeyError):
             reader = NXTomoReader(self.nx_fname, "/bad/data/path")  # noqa: F841
 
@@ -53,7 +35,7 @@ class TestNXReader:
         """
         Test NXTomoReader with simplest settings
         """
-        reader1 = NXTomoReader(self.nx_fname, self.nx_data_path)
+        reader1 = NXTomoReader(self.nx_fname)
         data1 = reader1.load_data()
         assert data1.shape == (self.data_desc.n_projs,) + self.data_desc.frame_shape
         assert np.allclose(data1[:, 0, 0], self.projs_vals)
@@ -62,15 +44,15 @@ class TestNXReader:
         """
         Test the data selection using "image_key".
         """
-        reader_projs = NXTomoReader(self.nx_fname, self.nx_data_path, image_key=ImageKey.PROJECTION.value)
+        reader_projs = NXTomoReader(self.nx_fname, image_key=ImageKey.PROJECTION.value)
         data = reader_projs.load_data()
         assert np.allclose(data[:, 0, 0], self.projs_vals)
 
-        reader_darks = NXTomoReader(self.nx_fname, self.nx_data_path, image_key=ImageKey.DARK_FIELD.value)
+        reader_darks = NXTomoReader(self.nx_fname, image_key=ImageKey.DARK_FIELD.value)
         data_darks = reader_darks.load_data()
         assert np.allclose(data_darks[:, 0, 0], self.darks_vals)
 
-        reader_flats = NXTomoReader(self.nx_fname, self.nx_data_path, image_key=ImageKey.FLAT_FIELD.value)
+        reader_flats = NXTomoReader(self.nx_fname, image_key=ImageKey.FLAT_FIELD.value)
         data_flats = reader_flats.load_data()
         assert np.allclose(data_flats[:, 0, 0], np.concatenate([self.flats1_vals, self.flats2_vals]))
 
@@ -83,10 +65,10 @@ class TestNXReader:
         def _check_correct_shape_succeeds(shape, sub_region, test_description=""):
             err_msg = "Something wrong with the following test:" + test_description
             data_buffer = np.zeros(shape, dtype="f")
-            reader1 = NXTomoReader(self.nx_fname, self.nx_data_path, sub_region=sub_region)
+            reader1 = NXTomoReader(self.nx_fname, sub_region=sub_region)
             data1 = reader1.load_data(output=data_buffer)
             assert id(data1) == id(data_buffer), err_msg
-            reader2 = NXTomoReader(self.nx_fname, self.nx_data_path, sub_region=sub_region)
+            reader2 = NXTomoReader(self.nx_fname, sub_region=sub_region)
             data2 = reader2.load_data()
             assert np.allclose(data1, data2), err_msg
 
@@ -124,7 +106,6 @@ class TestNXReader:
                     data_buffer_wrong_shape = np.zeros(wrong_shape, dtype="f")
                     reader = NXTomoReader(
                         self.nx_fname,
-                        self.nx_data_path,
                         sub_region=test_case["sub_region"],
                     )
                     reader.load_data(output=data_buffer_wrong_shape)
@@ -148,7 +129,7 @@ class TestNXReader:
         ]
 
         for test_case in test_cases:
-            reader = NXTomoReader(self.nx_fname, self.nx_data_path, sub_region=test_case["sub_region"])
+            reader = NXTomoReader(self.nx_fname, sub_region=test_case["sub_region"])
             data = reader.load_data()
             assert data.shape == test_case["expected_shape"]
             assert np.allclose(data[:, 0, 0], test_case["expected_values"])
@@ -156,7 +137,7 @@ class TestNXReader:
     def test_reading_with_binning_(self):
         from nabu.pipeline.reader import NXTomoReaderBinning
 
-        reader_with_binning = NXTomoReaderBinning((2, 2), self.nx_fname, self.nx_data_path)
+        reader_with_binning = NXTomoReaderBinning((2, 2), self.nx_fname)
         data = reader_with_binning.load_data()
         assert data.shape == (self.data_desc.n_projs,) + tuple(n // 2 for n in self.data_desc.frame_shape)
 
@@ -177,7 +158,6 @@ class TestNXReader:
         reader_distortion_corr = NXTomoReaderDistortionCorrection(
             distortion_corrector,
             self.nx_fname,
-            self.nx_data_path,
             sub_region=sub_region,
         )
 
@@ -220,7 +200,7 @@ class TestNXReader:
         for test_case in test_cases:
             binning = test_case.get("binning", None)
             reader_cls = NXTomoReader
-            init_args = [self.nx_fname, self.nx_data_path]
+            init_args = [self.nx_fname]
             init_kwargs = {"sub_region": test_case["sub_region"]}
             if binning is not None:
                 reader_cls = NXTomoReaderBinning
@@ -231,6 +211,29 @@ class TestNXReader:
             assert data.shape == test_case["expected_shape"], err_msg
             assert np.allclose(data[:, 0, 0], test_case["expected_values"]), err_msg
 
+    def test_load_exclude_projections(self):
+        n_z, n_x = self.data_desc.frame_shape
+        # projs_idx = np.where(self.image_key == 0)[0]
+        projs_idx = np.arange(self.data_desc.n_projs, dtype=np.int64)
+        excluded_projs_idx_1 = projs_idx[10:20]
+        excluded_projs_idx_2 = np.concatenate([projs_idx[10:14], projs_idx[50:57]])
+
+        set_to_nparray = lambda x: np.array(sorted(list(x)))
+
+        projs_idx1 = set_to_nparray(set(projs_idx) - set(excluded_projs_idx_1))
+        projs_idx2 = set_to_nparray(set(projs_idx) - set(excluded_projs_idx_2))
+
+        sub_regions_to_test = (
+            (projs_idx1, None, None),
+            (projs_idx1, slice(0, n_z // 2), None),
+            (projs_idx2, None, None),
+            (projs_idx2, slice(3, n_z // 2), None),
+        )
+        for sub_region in sub_regions_to_test:
+            reader = NXTomoReader(self.nx_fname, sub_region=sub_region)
+            data = reader.load_data()
+            assert np.allclose(data[:, 0, 0], self.projs_vals[sub_region[0]])
+
 
 @pytest.fixture(scope="class")
 def bootstrap_edf_reader(request):

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/misc/utils.py

@@ -3,9 +3,9 @@ import numpy as np
 
 def rescale_data(data, new_min, new_max, data_min=None, data_max=None):
     if data_min is None:
-        data_min = np.min(data)
+        data_min = np.nanmin(data)
     if data_max is None:
-        data_max = np.max(data)
+        data_max = np.nanmax(data)
     return (new_max - new_min) / (data_max - data_min) * (data - data_min) + new_min
 
 

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/pipeline/estimators.py

@@ -690,7 +690,7 @@ class CompositeCORFinder(CORFinderBase):
         tmp_sy, ovsd_sx = radio1.shape
         assert orig_sy == tmp_sy and orig_ovsd_sx == ovsd_sx, "this should not happen"
 
-        cor_side = self.cor_options["side"]
+        cor_side = self._lookup_side if self._lookup_side is not None else self.cor_options["side"]
         if cor_side == "center":
             overlap_min = max(round(ovsd_sx - ovsd_sx / 3), 4)
             overlap_max = min(round(ovsd_sx + ovsd_sx / 3), 2 * ovsd_sx - 4)

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/pipeline/fullfield/chunked.py

@@ -1,6 +1,5 @@
 from os import path
 from time import time
-from math import ceil
 import numpy as np
 from silx.io.url import DataUrl
 
@@ -127,10 +126,10 @@ class ChunkedPipeline:
         if len(chunk_shape) != 3:
             raise ValueError("Expected chunk_shape to be a tuple of length 3 in the form (n_z, n_y, n_x)")
         self.chunk_shape = tuple(int(c) for c in chunk_shape)  # cast to int, as numpy.int64 can make pycuda crash
-        # TODO: sanity check (eg. compare to size of radios in dataset_info) ?
+        ss_start = getattr(self.process_config, "subsampling_start", 0)
         # (n_a, n_z, n_x)
         self.radios_shape = (
-            ceil(self.chunk_shape[0] / self.process_config.subsampling_factor),
+            np.arange(self.chunk_shape[0])[ss_start :: self.process_config.subsampling_factor].size,
             self.chunk_shape[1] // self.process_config.binning[1],
             self.chunk_shape[2] // self.process_config.binning[0],
         )
@@ -340,13 +339,28 @@ class ChunkedPipeline:
             subs_z = None
             subs_x = None
             angular_sub_region = slice(*(self.sub_region[0]))
+
+            # exclude(subsample(.)) != subsample(exclude(.))
+            # Here we want the latter: first exclude the user-defined angular range, and then subsample the remaining indices
+            if len(self.dataset_info.get_excluded_projections_indices()) > 0:
+                angular_sub_region = np.array(
+                    [
+                        self.dataset_info.index_to_proj_number(i)
+                        for i in sorted(list(self.dataset_info.projections.keys()))
+                    ]
+                )
             if self.process_config.subsampling_factor:
                 subs_angles = self.process_config.subsampling_factor
-                angular_sub_region = slice(
-                    getattr(self.process_config, "subsampling_start", 0) + self.sub_region[0][0],
-                    self.sub_region[0][1],
-                    subs_angles,
-                )
+                start = getattr(self.process_config, "subsampling_start", 0) + self.sub_region[0][0]
+                if isinstance(angular_sub_region, slice):
+                    angular_sub_region = slice(
+                        start,
+                        self.sub_region[0][1],
+                        subs_angles,
+                    )
+                else:
+                    angular_sub_region = angular_sub_region[start::subs_angles]
+
             reader_sub_region = (
                 angular_sub_region,
                 slice(*(self.sub_region[1]) + ((subs_z,) if subs_z else ())),
@@ -363,7 +377,7 @@ class ChunkedPipeline:
             if self.dataset_info.kind == "nx":
                 self.chunk_reader = NXTomoReader(
                     self.dataset_info.dataset_hdf5_url.file_path(),
-                    self.dataset_info.dataset_hdf5_url.data_path(),
+                    data_path=self.dataset_info.dataset_hdf5_url.data_path(),
                     sub_region=reader_sub_region,
                     image_key=0,
                     **other_reader_kwargs,
@@ -865,9 +879,10 @@ class ChunkedPipeline:
             data_vwu[i] = self.radios[:, i, :]
         # ---
 
-        return self.reconstruction.reconstruct(  # pylint: disable=E1101
+        rec = self.reconstruction.reconstruct(  # pylint: disable=E1101
             data_vwu,
         )
+        return rec.astype("f")  # corrct uses float64 data
 
     @pipeline_step("histogram", "Computing histogram")
     def _compute_histogram(self, data=None):

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/pipeline/fullfield/nabu_config.py

@@ -103,7 +103,7 @@ nabu_config = {
         },
         "detector_distortion_correction": {
             "default": "",
-            "help": "Apply coordinate transformation on the raw data, at the reading stage. Default (empty) is None. Available are: None, identity(for testing the pipeline), map_xz. This latter method requires two URLs being passed by detector_distortion_correction_options: map_x and map_z pointing to two 2D arrays containing the position where each pixel can be interpolated at in the raw data",
+            "help": "Apply coordinate transformation on the raw data, at the reading stage. Default (empty) is None.\n Available are: None, identity(for testing the pipeline), map_xz.\n This latter method requires two URLs being passed by detector_distortion_correction_options: map_x and map_z pointing to two 2D arrays containing the position where each pixel can be interpolated at in the raw data",
             "validator": detector_distortion_correction_validator,
             "type": "advanced",
         },

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/pipeline/fullfield/processconfig.py

@@ -12,6 +12,7 @@ from ...resources.nxflatfield import update_dataset_info_flats_darks
 from ...resources.utils import get_quantities_and_units
 from ..estimators import estimate_cor
 from ..processconfig import ProcessConfigBase
+from ..config_validators import convert_to_bool
 from .nabu_config import nabu_config, renamed_keys
 from .dataset_validator import FullFieldDatasetValidator
 from nxtomo.nxobject.nxdetector import ImageKey
@@ -475,7 +476,7 @@ class ProcessConfig(ProcessConfigBase):
         # Double flat field
         #
         # ---- COMPAT  ----
-        if nabu_config["preproc"].get("double_flatfield_enabled", False):
+        if convert_to_bool(nabu_config["preproc"].get("double_flatfield_enabled", False))[0]:
             deprecation_warning(
                 "'double_flatfield_enabled' has been renamed to 'double_flatfield'. Please update your configuration file"
             )

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/pipeline/fullfield/reconstruction.py

@@ -367,6 +367,7 @@ class FullFieldReconstructor:
         # overlap = ceil(delta_z * d2 / (d1 + d2))  # sqrt(2) missing ?
 
         max_overlap = ceil(n_z * d2 / (d1 + d2))  # sqrt(2) missing ?
+        max_overlap = max(max_overlap, 10)  # use at least 10 pixels
 
         return (max_overlap, 0)
 

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/preproc/flatfield.py

@@ -456,10 +456,10 @@ class FlatFieldDataUrls(FlatField):
 
 
 class PCAFlatsNormalizer:
-    """This class implement a flatfield normalization based on a PCA of a series of acauired flatfields.
+    """This class implement a flatfield normalization based on a PCA of a series of acquired flatfields.
     The PCA decomposition is handled by a PCAFlatsDecomposer object.
 
-    This implementation was proposed by Jailin C. et al in https://doi.org/10.1107/S1600577516015812.
+    This implementation was proposed by Jailin C. et al in https://journals.iucr.org/s/issues/2017/01/00/fv5055/
 
     Code initially written by ID11 @ ESRF staff.
     Jonathan Wright - Implementation based on research paper
@@ -619,7 +619,7 @@ class PCAFlatsDecomposer:
     """This class implements a PCA decomposition of a serie of acquired flatfields.
     The PCA decomposition is used to normalize the projections through a PCAFLatNormalizer object.
 
-    This implementation was proposed by Jailin C. et al in https://doi.org/10.1107/S1600577516015812.
+    This implementation was proposed by Jailin C. et al in https://journals.iucr.org/s/issues/2017/01/00/fv5055/
 
     Code initially written by ID11 @ ESRF staff.
     Jonathan Wright - Implementation based on research paper

nabu-2025.1.1/nabu/reconstruction/iterative.py

@@ -0,0 +1,30 @@
+import numpy as np
+
+
+class IterativeBase:
+
+    backend = None  # placeholder
+    implementation = None  # placeholder
+
+    default_extra_options = {
+        "axis_correction": None,
+        "centered_axis": False,
+        "clip_outer_circle": False,
+        "scale_factor": None,
+        "outer_circle_value": 0.0,
+    }
+
+    backend_processing_class = ProcessingBase
+
+    def __init__(
+        self,
+        sino_shape,
+        angles=None,
+        rot_center=None,
+        halftomo=False,
+        filter_name=None,
+        slice_roi=None,
+        scale_factor=None,
+        extra_options=None,
+        backend_options=None,
+    ): ...

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/resources/dataset_analyzer.py

@@ -396,6 +396,11 @@ class EDFDatasetAnalyzer(DatasetAnalyzer):
     def scan_dirname(self):
         return self.dataset_scanner.path
 
+    def get_excluded_projections_indices(self, including_other_frames_types=True):
+        if not (including_other_frames_types):
+            raise NotImplementedError
+        return self.dataset_scanner.get_ignored_projection_indices()
+
 
 class HDF5DatasetAnalyzer(DatasetAnalyzer):
     """
@@ -606,6 +611,36 @@ class HDF5DatasetAnalyzer(DatasetAnalyzer):
     def get_frame(self, idx):
         return get_data(self.dataset_scanner.frames[idx].url)
 
+    def get_frames_indices(self, frame_type):
+        return self._select_according_to_frame_type(np.arange(self.dataset_scanner.image_key_control.size), frame_type)
+
+    def index_to_proj_number(self, proj_index):
+        """
+        Return the projection *number*, from its frame *index*.
+
+        For example if there are 11 flats before projections,
+        then projections will have indices [11, 12, .....] (possibly not contiguous)
+        while their number is [0, 1, ..., ] (contiguous, starts from 0)
+        """
+        all_projs_indices = self.get_frames_indices("projection")
+        return search_sorted(all_projs_indices, proj_index)
+
+    def get_excluded_projections_indices(self, including_other_frames_types=True):
+        # Get indices of ALL projections (even excluded ones)
+        # the index accounts for flats/darks !
+        # Get indices of excluded projs (again, accounting for flats/darks)
+        ignored_projs_indices = self.dataset_scanner.get_ignored_projection_indices()
+        ignored_projs_indices = [
+            idx for idx in ignored_projs_indices if self.dataset_scanner.frames[idx].is_control is False
+        ]
+        if including_other_frames_types:
+            return ignored_projs_indices
+        # Get indices of excluded projs, now relative to the pure projections stack
+        ignored_projs_indices_rel = [
+            self.index_to_proj_number(ignored_proj_idx_abs) for ignored_proj_idx_abs in ignored_projs_indices
+        ]
+        return ignored_projs_indices_rel
+
 
 def get_angle_at_index(all_angles, index):
     """

nabu-2025.1.1/nabu/resources/tests/test_dataset_analyzer.py

@@ -0,0 +1,37 @@
+import pytest
+import numpy as np
+from nabu.testutils import get_dummy_nxtomo_info
+from nabu.resources.dataset_analyzer import analyze_dataset
+
+
+@pytest.fixture(scope="class")
+def bootstrap_nx(request):
+    cls = request.cls
+    cls.nx_fname, cls.data_desc, cls.image_key, cls.projs_vals, cls.darks_vals, cls.flats1_vals, cls.flats2_vals = (
+        get_dummy_nxtomo_info()
+    )
+
+
+@pytest.mark.usefixtures("bootstrap_nx")
+class TestNXDataset:
+
+    def test_exclude_projs_angular_range(self):
+        dataset_info_with_all_projs = analyze_dataset(self.nx_fname)
+
+        # Test exclude angular range - angles min and max in degrees
+        angular_ranges_to_test = [(0, 15), (5, 6), (50, 58.5)]
+        for angular_range in angular_ranges_to_test:
+            angle_min, angle_max = angular_range
+            dataset_info = analyze_dataset(
+                self.nx_fname,
+                extra_options={"exclude_projections": {"type": "angular_range", "range": [angle_min, angle_max]}},
+            )
+            excluded_projs_indices = dataset_info.get_excluded_projections_indices()
+            # Check that get_excluded_projections_indices() angles are correct
+            for excluded_proj_index in excluded_projs_indices:
+                frame_angle_deg = dataset_info.dataset_scanner.frames[excluded_proj_index].rotation_angle
+                assert angle_min <= frame_angle_deg and frame_angle_deg <= angle_max
+
+            assert set(dataset_info_with_all_projs.projections.keys()) - set(dataset_info.projections.keys()) == set(
+                excluded_projs_indices
+            )

{nabu-2025.1.0rc5 → nabu-2025.1.1}/nabu/testutils.py

@@ -1,3 +1,4 @@
+from dataclasses import dataclass
 from itertools import product
 import tarfile
 import os
@@ -5,6 +6,7 @@ import numpy as np
 from scipy.signal.windows import gaussian
 from silx.resources import ExternalResources
 from silx.io.dictdump import nxtodict, dicttonx
+from nxtomo.application.nxtomo import ImageKey
 
 utilstest = ExternalResources(
     project="nabu", url_base="http://www.silx.org/pub/nabu/data/", env_key="NABU_DATA", timeout=60
@@ -56,6 +58,38 @@ def get_data(*dataset_path):
     return np.load(dataset_downloaded_path)
 
 
+@dataclass
+class SimpleNXTomoDescription:
+    n_darks: int = 0
+    n_flats1: int = 0
+    n_projs: int = 0
+    n_flats2: int = 0
+    n_align: int = 0
+    frame_shape: tuple = None
+    dtype: np.dtype = np.uint16
+
+
+def get_dummy_nxtomo_info():
+    nx_fname = utilstest.getfile("dummy_nxtomo.nx")
+    data_desc = SimpleNXTomoDescription(
+        n_darks=10, n_flats1=11, n_projs=100, n_flats2=11, n_align=12, frame_shape=(11, 10), dtype=np.uint16
+    )
+    image_key = np.concatenate(
+        [
+            np.zeros(data_desc.n_darks, dtype=np.int32) + ImageKey.DARK_FIELD.value,
+            np.zeros(data_desc.n_flats1, dtype=np.int32) + ImageKey.FLAT_FIELD.value,
+            np.zeros(data_desc.n_projs, dtype=np.int32) + ImageKey.PROJECTION.value,
+            np.zeros(data_desc.n_flats2, dtype=np.int32) + ImageKey.FLAT_FIELD.value,
+            np.zeros(data_desc.n_align, dtype=np.int32) + ImageKey.ALIGNMENT.value,
+        ]
+    )
+    projs_vals = np.arange(data_desc.n_projs) + data_desc.n_flats1 + data_desc.n_darks
+    darks_vals = np.arange(data_desc.n_darks)
+    flats1_vals = np.arange(data_desc.n_darks, data_desc.n_darks + data_desc.n_flats1)
+    flats2_vals = np.arange(data_desc.n_darks, data_desc.n_darks + data_desc.n_flats2)
+    return nx_fname, data_desc, image_key, projs_vals, darks_vals, flats1_vals, flats2_vals
+
+
 def get_array_of_given_shape(img, shape, dtype):
     """
     From a given image, returns an array of the wanted shape and dtype.

{nabu-2025.1.0rc5 → nabu-2025.1.1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc5
+Version: 2025.1.1
 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>