nabu 2025.1.0rc6__py3-none-any.whl → 2025.1.1__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2025.1.0-rc6"
+__version__ = "2025.1.1"
 __nabu_modules__ = [
     "app",
     "cuda",

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/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/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/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/pipeline/fullfield/chunked.py

@@ -879,9 +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/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/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/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-2025.1.0rc6.dist-info → nabu-2025.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nabu
-Version: 2025.1.0rc6
+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-2025.1.0rc6.dist-info → nabu-2025.1.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=EGKVb44QFboUSoFCqFcSfj8VLtWXW3czbgYHuNnE_-I,274
+nabu/__init__.py,sha256=cquIT6AKfmVtn7EkXyjYjG8hLJ0tMLDKmD2vmBh_vnY,270
 nabu/tests.py,sha256=hOJD1GGxn_KE1bWMoxfjnjzI7d9JBUpoc9B2_tVFiEk,1370
 nabu/testutils.py,sha256=4I62IP3VLOJx8JvGBgY1t4i4CiJMWfT_aUopxg39JIM,10047
 nabu/utils.py,sha256=tJI64BNXMhD6W293fwwcgf9bvTalYG_5AwVGYkgi6tU,27179
@@ -69,7 +69,7 @@ nabu/estimation/cor.py,sha256=8RsyZ_MYT04EWvP2tLThftn_bD3cz9-uWo8D5FpXLKQ,50353
 nabu/estimation/cor_sino.py,sha256=qN6y16UVqoDX696JYyn3iWXDxQo0FMcFTuGbT92BW_s,18959
 nabu/estimation/distortion.py,sha256=DEXizQpgHBXmrhbQ0kuEchicxmiDgmU2qrh8bCgSezg,4701
 nabu/estimation/focus.py,sha256=CdtMFk6Xt4qq1JwwKDmDcVCeVocz-mpV0saikO0B1mc,17995
-nabu/estimation/motion.py,sha256=8fgwGsJMZleUugCCMRyZ2Zfi6-fWp-_dJpUnvetxGvk,26501
+nabu/estimation/motion.py,sha256=5p6Tsea-77Kc9QaYKkD33aQ_ZA5mSO1arHQ4tjclEJ0,26927
 nabu/estimation/tilt.py,sha256=6R8l8gnf00m-xdgLhvQmkvZ3lIO_8hDglNsFjzlzZ4E,8834
 nabu/estimation/translation.py,sha256=qoxT8VT38TZqrqLRwOef7-wBE5OeEObp_Qy9T2De2Do,10184
 nabu/estimation/utils.py,sha256=31d17Ng__NxcLOtGXPmbPPW1veh1m0poCvRgDCJssUA,347
@@ -81,7 +81,7 @@ nabu/estimation/tests/test_motion_estimation.py,sha256=WKUpkVand8VszoBIvsaEnhKqv
 nabu/estimation/tests/test_tilt.py,sha256=KIgTJqQvNfWndm8f3aRSdznWFl3AdQhYXiZPKLseYOs,1672
 nabu/estimation/tests/test_translation.py,sha256=RkOnCYgk9DZGKlIka1snqTv4wbIz_nG7-EHAxnBHsJU,2999
 nabu/io/__init__.py,sha256=AbQgj4-fCCHOKynO_PyAR9ejnFSuWKgroxxhxWVpjyQ,120
-nabu/io/cast_volume.py,sha256=eJuiKuZILD3xClUtYOjCqmwnbW12gwg-gJTzj606u_Y,21499
+nabu/io/cast_volume.py,sha256=y7MRsrC5WBbY0BtlnqQJWxByEP43Gq1qrq969bADGBI,22220
 nabu/io/detector_distortion.py,sha256=qO1Z6gejkBrixThvU_sLwH3UfLAe8aAO63YQ8z7PH78,11750
 nabu/io/reader.py,sha256=CRQfzLqG10QNzKpPY1j3z2toEAti2bNgImMwWnHQfVE,41775
 nabu/io/reader_helical.py,sha256=q3LOmu6F_4Uxi3rZZWJ-rsix2Lgu_saXXdiJF8TLi24,4533
@@ -109,7 +109,7 @@ nabu/misc/transpose.py,sha256=ogJ1PPYO0sOPUfCgjk-Ho5cTjlBbP-KXGqhCgTj75DY,223
 nabu/misc/unsharp.py,sha256=3xYsdiLTqTDlE8G-tIY7EeTf3nKxPrvMHOnXgkcKWvU,209
 nabu/misc/unsharp_cuda.py,sha256=-csDxfQt_naYn5O8fOxksYNqyFKxbF8lV7yXlPd2XoM,235
 nabu/misc/unsharp_opencl.py,sha256=HCPoobPwi2LEAfqGQ2qekjQi6G2VDKmqJQZTDXySv1Y,252
-nabu/misc/utils.py,sha256=s8ACtKdw9rTmlD0APdrpeo_ZIneKsTv2Xq3X2TRxCRk,3898
+nabu/misc/utils.py,sha256=b0JlnRmhEyx-9SBycRGQxPqNa25uTZqOFtGOF3Fyxdg,3904
 nabu/misc/tests/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 nabu/misc/tests/test_binning.py,sha256=vcZZINi_v_KOw4DMqLIgPlF-CwLTG102Yf7dMQ5_SEo,1890
 nabu/misc/tests/test_interpolation.py,sha256=H8ZJ7dppCcpxVa9wOBkJ9U0mymH5lGyCJ0LZCYIK8PE,2389
@@ -134,21 +134,21 @@ nabu/pipeline/config_validators.py,sha256=Wx9nnUpfxTJ8H2ODkUyjImTtJS9V68TafLH1Te
 nabu/pipeline/datadump.py,sha256=tKW-Dl28FU2vf1OuIie_YI1-GT1DMreis57sOR-DuGU,7026
 nabu/pipeline/dataset_validator.py,sha256=etQw9NC_YGsdWCgjsn8aJ3WfvcRuJlLVZlWoqhvvo-8,9263
 nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdSDUtzFUC1A_sS8jME,920
-nabu/pipeline/estimators.py,sha256=ALzlcBxaVMt7OprEgndfBE_csuv9aKZax3erD3nBWU0,51786
+nabu/pipeline/estimators.py,sha256=GhBs5bW4J2ZgDK30Pgg-hcb-B6SYQUPIP5sZmQhBpYA,51842
 nabu/pipeline/params.py,sha256=UKMQWFQnrlNMW5aIGty-JoGmBdkS6tpoAXCjW8n6FX8,4229
 nabu/pipeline/processconfig.py,sha256=3xx2Lc8uEzPAqSMwUncr4RCiCtKn2c7wnXXbPSn8GNo,7719
 nabu/pipeline/reader.py,sha256=wkxPHYOi_C8dHNc7kddB8AMtFuW7GjsP_tm6SJeHlEY,4792
 nabu/pipeline/utils.py,sha256=5GGhT9Wu7tHDlF3w7YNjTTYkNBl5xHa9EcRZSGFUWtM,3538
 nabu/pipeline/writer.py,sha256=NVeAtkWDtXg5UJ4C3wsbkfM23ZnK64atCWl8tjmjsuY,8166
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/fullfield/chunked.py,sha256=gEm9XYk1MhNQBi-2VSVrXKQD55XmLPQAoHn9sCsEDIc,43272
+nabu/pipeline/fullfield/chunked.py,sha256=5dGoP_vCajI7kl2b9AysufG6DV1gdX9uvF0THrhNDaA,43330
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=US5prrhNjsx3QVHkY5duQp8uFcGdgYEPzVS7nfWkJRw,6047
 nabu/pipeline/fullfield/computations.py,sha256=uqf7LvuDPm7n51BpP8eb8vTewDgRFyzSDP249g3FWBE,10098
 nabu/pipeline/fullfield/dataset_validator.py,sha256=HK_bmlII9pc59PXCgKJOyLv7Xu3DYv_jbH3RmQSgzvI,2933
 nabu/pipeline/fullfield/get_double_flatfield.py,sha256=uYFDAii6Nw4RCUQO_6Id6tXLdmtVbj_pxAHQWennSeE,5411
-nabu/pipeline/fullfield/nabu_config.py,sha256=F1E4KwHTfw6tynBnBjvr1F6tflIFsvDp8Pyop7xNmGg,33146
+nabu/pipeline/fullfield/nabu_config.py,sha256=XcvPpJjyTmp8QSWK1lcNWRa1ybL0AQ0poj3O_CgDYtM,33150
 nabu/pipeline/fullfield/processconfig.py,sha256=72hjxgClKcxmzypVpvcWzkzoXP7Ypu5VpRxMjYQVnJQ,38461
-nabu/pipeline/fullfield/reconstruction.py,sha256=cljRyxD8rvZ5qDws_5AwChi7P-5T_0SSXsGkYUGOVb8,38006
+nabu/pipeline/fullfield/reconstruction.py,sha256=Fi3GCsVjO3CpYIWZM-4i6S2UOzG7iqVeukQ375j09Pg,38075
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=HdKjUSj3PIpJb1dKSzJg8s4zXbAnMPWaPn8kvp_xQEs,657
 nabu/pipeline/helical/fbp.py,sha256=MKn587bO5Lj7yFu-Sll2RkOIY5r3rC-fmC10SzFU5i0,5841
@@ -235,6 +235,7 @@ nabu/reconstruction/filtering.py,sha256=monJnA_kk9k_Gy7bMAos9I-XgU8czWhf9vBth6ik
 nabu/reconstruction/filtering_cuda.py,sha256=_S-BZMhtnNt8ugePSmf-LF7JvMPCOyGPUMSseymgwZw,4019
 nabu/reconstruction/filtering_opencl.py,sha256=v-sUzbnRp6M1B221F-iSh-crBCGknjHYYsjFs05VhDY,3788
 nabu/reconstruction/hbp.py,sha256=Qll7i20LWxUo1-SHRxemkYAolBTP8HScwt1OvWmD2r0,18642
+nabu/reconstruction/iterative.py,sha256=urZg_Aj3P2wGfsbjlyvmOvf2yd-kXNt_f4Sjlj6oxhE,637
 nabu/reconstruction/mlem.py,sha256=wgC2pKl6RKB-f2318worB9VE-qCGoQcz24aKbtkrJos,5794
 nabu/reconstruction/projection.py,sha256=SNocaOY9HuNiHs-VxkW9IS707JPJnd3sDjAbf7aIw2E,9081
 nabu/reconstruction/reconstructor.py,sha256=16xxHcK4iie-uh-trf6x_IuvgxJKBvQRTE5B8tnc4F8,7358
@@ -318,9 +319,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=Khe4zFf0kRzu65Yxnvq58gt1ljOztqJGdMDhVAiM7lM,24363
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2025.1.0rc6.dist-info/licenses/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2025.1.0rc6.dist-info/METADATA,sha256=yA0Om_mA72YwMBuAcOrLfV5_PjGK375QUsRrnp1gE50,4274
-nabu-2025.1.0rc6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nabu-2025.1.0rc6.dist-info/entry_points.txt,sha256=YxzCY5CNQ1XHrIGbRKg-BgC1Jy7QaCITdITpyhhxpZU,1338
-nabu-2025.1.0rc6.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2025.1.0rc6.dist-info/RECORD,,
+nabu-2025.1.1.dist-info/licenses/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2025.1.1.dist-info/METADATA,sha256=3wyX7ZF2Sqn5Z_w80g6_dvSEeT6Uct06l8DvCoYRxpA,4271
+nabu-2025.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nabu-2025.1.1.dist-info/entry_points.txt,sha256=YxzCY5CNQ1XHrIGbRKg-BgC1Jy7QaCITdITpyhhxpZU,1338
+nabu-2025.1.1.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2025.1.1.dist-info/RECORD,,