nabu 2024.1.6__py3-none-any.whl → 2024.1.7__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.6"
+__version__ = "2024.1.7"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/fullfield/chunked.py

@@ -548,7 +548,6 @@ class ChunkedPipeline:
 
         if options["method"] == "FBP":
             n_slices = self.n_slices
-            radios_shape_for_sino_builder = self.radios_cropped_shape
             self.reconstruction = self.FBPClass(
                 self.sinos_shape[1:],
                 angles=options["angles"],
@@ -567,7 +566,6 @@ class ChunkedPipeline:
             )
 
         if options["method"] == "cone":
-            radios_shape_for_sino_builder = self.radios_shape
             n_slices = self.n_slices + sum(self.margin[0])
             # For numerical stability, normalize all lengths with respect to detector pixel size
             pixel_size_m = self.dataset_info.pixel_size * 1e-6
@@ -586,8 +584,6 @@ class ChunkedPipeline:
         self._allocate_recs(*self.process_config.rec_shape, n_slices=n_slices)
         n_a, _, n_x = self.radios_cropped_shape
         self._tmp_sino = self._allocate_array((n_a, n_x), "f", name="tmp_sino")
-        if options["method"] == "cone":
-            self.sinos = self._allocate_array(self.sino_builder.output_shape, "f", name="sinos")
 
     @use_options("histogram", "histogram")
     def _init_histogram(self):
@@ -734,14 +730,21 @@ class ChunkedPipeline:
         """
         This reconstructs the entire sinograms stack at once
         """
-        self.sino_builder.get_sinos(self.radios, output=self.sinos)
+
+        n_angles, n_z, n_x = self.radios.shape
+        # can't do a discontiguous single copy...
+        sinos_contig = self._allocate_array((n_z, n_angles, n_x), np.float32, "sinos_cone")
+        for i in range(n_z):
+            sinos_contig[i] = self.radios[:, i, :]
+        #
+
         z_min, z_max = self.sub_region_xz[2:]
-        n_z = self.process_config.radio_shape(binning=True)[0]
+        n_z_tot = self.process_config.radio_shape(binning=True)[0]
 
         self.reconstruction.reconstruct(  # pylint: disable=E1101
-            self.sinos,
+            sinos_contig,
             output=self.recs,
-            relative_z_position=((z_min + z_max) / self.process_config.binning_z / 2) - n_z / 2,
+            relative_z_position=((z_min + z_max) / self.process_config.binning_z / 2) - n_z_tot / 2,
         )
 
     @pipeline_step("histogram", "Computing histogram")

nabu/pipeline/fullfield/dataset_validator.py

@@ -29,7 +29,7 @@ class FullFieldDatasetValidator(DatasetValidatorBase):
     def _check_slice_indices(self):
         nx, nz = self.dataset_info.radio_dims
         rec_params = self.rec_params
-        if rec_params["enable_halftomo"]:
+        if self.is_halftomo:
             ny, nx = self._get_nx_ny()
         what = (("start_x", "end_x", nx), ("start_y", "end_y", nx), ("start_z", "end_z", nz))
         for start_name, end_name, numels in what:
@@ -61,3 +61,7 @@ class FullFieldDatasetValidator(DatasetValidatorBase):
                 self.logger.warning(
                     "Cone-beam reconstruction: 'sample_detector_dist' not provided, will use the one in dataset metadata"
                 )
+            if self.is_halftomo:
+                err_msg = "Cone-beam reconstruction with half-acquisition is not supported yet"
+                self.logger.fatal(err_msg)
+                raise NotImplementedError(err_msg)

nabu/pipeline/fullfield/processconfig.py

@@ -600,7 +600,7 @@ class ProcessConfig(ProcessConfigBase):
             )
             if all([m is not None for m in mean_positions_xyz]):
                 rec_options["position"] = mean_positions_xyz
-            if rec_options["sample_detector_dist"] is None:
+            if rec_options["method"] == "cone" and rec_options["sample_detector_dist"] is None:
                 rec_options["sample_detector_dist"] = self.dataset_info.distance  # was checked to be not None earlier
 
             # New key

nabu/pipeline/helical/tests/test_accumulator.py

@@ -1,5 +1,5 @@
 from nabu.pipeline.helical import gridded_accumulator, span_strategy
-from nabu.testutils import get_data
+from nabu.testutils import get_data, __do_long_tests__
 
 import pytest
 import numpy as np
@@ -49,6 +49,7 @@ def bootstrap(request):
     cls.rtol_regridded = 1.0e-6
 
 
+@pytest.mark.skipif(not (__do_long_tests__), reason="need environment variable NABU_LONG_TESTS=1")
 @pytest.mark.usefixtures("bootstrap")
 class TestGriddedAccumulator:
     """

nabu/pipeline/processconfig.py

@@ -181,7 +181,10 @@ class ProcessConfigBase:
         #
         if isinstance(tilt, str):  # auto-tilt
             self.tilt_estimator = DetectorTiltEstimator(
-                self.dataset_info, logger=self.logger, autotilt_options=self.nabu_config["preproc"]["autotilt_options"]
+                self.dataset_info,
+                do_flatfield=self.nabu_config["preproc"]["flatfield"],
+                logger=self.logger,
+                autotilt_options=self.nabu_config["preproc"]["autotilt_options"],
             )
             tilt = self.tilt_estimator.find_tilt(tilt_method=tilt)
         self.dataset_info.detector_tilt = tilt

nabu/processing/tests/test_fftshift.py

@@ -31,6 +31,7 @@ def bootstrap(request):
         cls.cu_ctx.pop()
 
 
+@pytest.mark.skip(reason="OpenCL fftshift is a prototype")
 @pytest.mark.usefixtures("bootstrap")
 class TestFFTshift:
     def _do_test_fftshift(self, config, fftshift_cls):

nabu/reconstruction/tests/test_deringer.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 from nabu.reconstruction.rings_cuda import CudaSinoMeanDeringer
-from nabu.testutils import compare_arrays, get_data, generate_tests_scenarios, __do_long_tests__
+from nabu.testutils import compare_arrays, get_data, generate_tests_scenarios, __do_long_tests__, __do_large_mem_tests__
 from nabu.reconstruction.rings import MunchDeringer, SinoMeanDeringer, VoDeringer, __has_algotom__
 from nabu.thirdparty.pore3d_deringer_munch import munchetal_filter
 from nabu.cuda.utils import __has_pycuda__, get_cuda_context
@@ -144,8 +144,8 @@ class TestMunchDeringer:
         # TODO check result. The generated test sinogram is "too synthetic" for this kind of deringer
 
     @pytest.mark.skipif(
-        not (__have_tomocupy_deringer__),
-        reason="Need cupy for this test",
+        not (__have_tomocupy_deringer__ and __do_large_mem_tests__),
+        reason="Need cupy for this test, and use NABU_LARGE_MEM_TESTS",
     )
     def test_cuda_vo_deringer(self):
         # Beware, this deringer seems to be buggy for "too-small" sinograms

nabu/reconstruction/tests/test_halftomo.py

@@ -3,10 +3,11 @@ import pytest
 from nabu.testutils import get_data, generate_tests_scenarios, compare_shifted_images
 from nabu.cuda.utils import get_cuda_context, __has_pycuda__, __has_cufft__
 from nabu.opencl.utils import get_opencl_context, __has_pyopencl__
+from nabu.processing.fft_opencl import has_vkfft as has_vkfft_cl
 from nabu.thirdparty.algotom_convert_sino import extend_sinogram
 
 __has_pycuda__ = __has_pycuda__ and __has_cufft__  # need both for using Cuda backprojector
-
+__has_pyopencl__ = __has_pyopencl__ and has_vkfft_cl()
 
 if __has_pycuda__:
     from nabu.reconstruction.fbp import CudaBackprojector

{nabu-2024.1.6.dist-info → nabu-2024.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.6
+Version: 2024.1.7
 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-2024.1.6.dist-info → nabu-2024.1.7.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=R001g25kFvEVDDeajbatTdAG1ufFI08DldAcf4ADwF4,270
+nabu/__init__.py,sha256=syNuJVNxIJSDQ2NM6gqCh37LvuExshXotfyhoQEwQhc,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
 nabu/utils.py,sha256=w-xfRb6TFQpS-tao6nlvfmr962pmeec-WH1GltSUCrk,23767
@@ -132,16 +132,16 @@ nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdS
 nabu/pipeline/estimators.py,sha256=4V5pwl5vUFMJDanWnmw7POnSsa9lKyKtUzvq9GLcJwc,41374
 nabu/pipeline/fallback_utils.py,sha256=7ccrKYE-rp3fydb72VA6W0_eKcEoqYBEAPlmij_lyEc,6086
 nabu/pipeline/params.py,sha256=VdrekcxOnbrMzvvLcwEWINiMM0uVKmPxJJBwp3lhHBg,3479
-nabu/pipeline/processconfig.py,sha256=3wCobeC_gI9OTO7v0Hk-IeEJUdKoavK-OzKLd1da5Dg,8216
+nabu/pipeline/processconfig.py,sha256=O0phgvfWtL9bg3_GE3cw9MZXS8PUy8z2rzhpoqP9U84,8320
 nabu/pipeline/utils.py,sha256=NONAgBfTfUYvBNfoTqD33MAYaPZyCJL10SnR6B0lLec,3462
 nabu/pipeline/writer.py,sha256=0ts40VNN3RiRURvZ2gNqsigsAJuwcjnYF4RJ15qaMpI,7558
 nabu/pipeline/fullfield/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/fullfield/chunked.py,sha256=qGE9gpww2zPbtPeM1Fe0RPRhl3onqxs8fr3HRug-x6I,36919
+nabu/pipeline/fullfield/chunked.py,sha256=DdmSXI9BnWPrXG99MbzqQdJrh0DHlkuM8Dnv5xWkcM0,36873
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=aGzjY8MX6OL8auEj6Y0RfOGCmFnczsdfj6-8Net5AbQ,5645
 nabu/pipeline/fullfield/computations.py,sha256=VpIURVXh8EpNSfait_AIFM4Ci-GK_546Wkb-Wn9r31Y,9935
-nabu/pipeline/fullfield/dataset_validator.py,sha256=sRgUECUc8aOjFbwrW-dHjvIf7K3T40YPSIgt3cInKAc,3055
+nabu/pipeline/fullfield/dataset_validator.py,sha256=8B2lB9j7elF_NmOOOyr8UADVfC15Oofzy2AyWoPufQM,3265
 nabu/pipeline/fullfield/nabu_config.py,sha256=a0mMoLkvlvHgX6RmUS1m1UhJS-XB3O6wBCnkNoI90Cs,30358
-nabu/pipeline/fullfield/processconfig.py,sha256=ad2lmo-cCkzfDJqMd__FhbfIInndTxQsLdgH9Ec9Tzc,36107
+nabu/pipeline/fullfield/processconfig.py,sha256=TKQeHyImp5blhP4_lve8g5voDjSKAMNv7kelyB3e698,36143
 nabu/pipeline/fullfield/reconstruction.py,sha256=Km_ZDtoiDQdX3TdTh6E9bzS5hoMC0jYU5eZWodaLbIg,36627
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
@@ -158,7 +158,7 @@ nabu/pipeline/helical/span_strategy.py,sha256=7zV_Oo_liFiuv6m70o08XyoEIo_7QYs7MV
 nabu/pipeline/helical/utils.py,sha256=51Qbh8db6-DX0iB9B9Kb07uwIG6_upAJg_8nhyzbB7o,1555
 nabu/pipeline/helical/weight_balancer.py,sha256=j0TGe50tbbsilQvml9CgMxeSy83CNaifHj-xuMGl8uE,3981
 nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nabu/pipeline/helical/tests/test_accumulator.py,sha256=nNHwqUgSyUpdZVYNVyxqekj0SoThCF8s-8o3NfSw6vI,6416
+nabu/pipeline/helical/tests/test_accumulator.py,sha256=DCwTAWQLdUNJBJpjhHT8o1gLbznpuj_zqbQOfQnrShw,6534
 nabu/pipeline/helical/tests/test_pipeline_elements_full.py,sha256=zeR9SaeD0mnhtKU7qo4Qrn_lg1I1Vhg4dqzj6jy8tpg,14569
 nabu/pipeline/helical/tests/test_strategy.py,sha256=rt8SsUHBMMcVFl48kRGcOyf1y4bYqaA2xDznQxE7wFs,2721
 nabu/pipeline/tests/test_chunk_reader.py,sha256=OB279hSvgmVhWv_OauZNWTJeaaiheETayGYK79Op10Q,3410
@@ -213,7 +213,7 @@ nabu/processing/unsharp_cuda.py,sha256=tbgw3selI4x4qsSxyQJ8Q4HUxdEBbZOJtSys-0yzj
 nabu/processing/unsharp_opencl.py,sha256=ikmZhQB-kji3UFrvFzHJNvDUpaVSpzcCJRX_bqSQeGQ,2637
 nabu/processing/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nabu/processing/tests/test_fft.py,sha256=zDGDTXZjHBVbiVFiQfkrkYFFMyotJRFU-KgoNm1FGms,9827
-nabu/processing/tests/test_fftshift.py,sha256=90QlNO62pN9P_oY54JYrPX5pLjzO5SSC4ZEyr5F__hQ,2559
+nabu/processing/tests/test_fftshift.py,sha256=-XgJUm0eF3D-rMTlI9u3jaWYIlPFZEpM0PwW3SMDLG0,2618
 nabu/processing/tests/test_histogram.py,sha256=25CLs1WZpLF9xZ2DR82x4_YokA5Z76Qsnn6zY8YdJj8,2283
 nabu/processing/tests/test_medfilt.py,sha256=lVfLWIxWiLfODFc14WYbq1W02rgQDtCnrSgXnWgU6yU,2722
 nabu/processing/tests/test_muladd.py,sha256=cRhAC5hgmRV0BAwPA4o4M-kcx-UDniLK7sSyiN0F3kE,1927
@@ -240,10 +240,10 @@ nabu/reconstruction/sinogram_cuda.py,sha256=wS84AIy3T00d1kTtuJOQmA3hktbDVs4ybwB9
 nabu/reconstruction/sinogram_opencl.py,sha256=p793N26VknU8KIZLtDgFY6HNx0TylemZ1YL4WKD3fHs,1403
 nabu/reconstruction/tests/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 nabu/reconstruction/tests/test_cone.py,sha256=R9Q-o9jz5ZBRwpGRRDwWr4owrrI3bJow5f_x_toq_lw,11813
-nabu/reconstruction/tests/test_deringer.py,sha256=u7HTMKH0DiZ1JAs68svi7eOCQt_sgxpXH6RQ12rDaVE,8299
+nabu/reconstruction/tests/test_deringer.py,sha256=C5wj6RNzmpt_Cry4fonC8KXWvgPpcXfRbG8Bex_30S4,8380
 nabu/reconstruction/tests/test_fbp.py,sha256=p80zPCZkgJpERpqG5HHfbtbHBeqJUT8WY-q6FXOJJ7M,10053
 nabu/reconstruction/tests/test_filtering.py,sha256=PFJLQMDBQo-UuS_CfKrWZ_DdHarmVlcbsiZ_kmToWXY,4782
-nabu/reconstruction/tests/test_halftomo.py,sha256=rdPY4oL8JTJqDzpn-pdqjDp72pN39-5DipKqBTyyBxo,4171
+nabu/reconstruction/tests/test_halftomo.py,sha256=j-vq9Oyxl7dYGuAMMO2G-Y7EcryD1RGEyXqmycc0o_8,4290
 nabu/reconstruction/tests/test_projector.py,sha256=W4zntShzL47HjMGQG11zIYzMXwX0KfMN4BVIAapdy_I,6033
 nabu/reconstruction/tests/test_reconstructor.py,sha256=dEGqlQHfFwX_V2Ybnq5AAM5tprXn_2OuCSrC6cW4S0A,3221
 nabu/reconstruction/tests/test_sino_normalization.py,sha256=fGv5Dlidxgm8ZC70Nk6oqVgpY2jzOW9NJaGlo44IJOo,3692
@@ -288,9 +288,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
 nabu/thirdparty/tomocupy_remove_stripe.py,sha256=VgXHr2tzTAAGZix5pwhFfbPxj4tt3yXBcjCPNQSLPAg,22810
 nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
 nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
-nabu-2024.1.6.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.1.6.dist-info/METADATA,sha256=ogaBqKAavm40N8GeX3XPDsRTwKm12-BgSfbB3HuR7ag,5224
-nabu-2024.1.6.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.1.6.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.1.6.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.1.6.dist-info/RECORD,,
+nabu-2024.1.7.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.7.dist-info/METADATA,sha256=_Bv8vjCsYa3a926AT-jJHgEkvMprSL5LYjRNDbhzpiA,5224
+nabu-2024.1.7.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+nabu-2024.1.7.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.7.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.7.dist-info/RECORD,,