nabu 2024.1.6__tar.gz → 2024.1.7__tar.gz

{nabu-2024.1.6/nabu.egg-info → nabu-2024.1.7}/PKG-INFO

@@ -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 → nabu-2024.1.7}/nabu/__init__.py

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

{nabu-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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-2024.1.6 → nabu-2024.1.7}/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 → nabu-2024.1.7/nabu.egg-info}/PKG-INFO

@@ -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 → nabu-2024.1.7}/nabu.egg-info/top_level.txt

@@ -1,3 +1,4 @@
+build
 dist
 doc
 nabu