nabu 2024.2.4__py3-none-any.whl → 2024.2.5__py3-none-any.whl

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.4"
+__version__ = "2024.2.5"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/cuda/src/cone.cu

@@ -26,23 +26,33 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 */
 
 
-static const unsigned int g_anglesPerWeightBlock = 16;
-static const unsigned int g_detBlockU = 32;
-static const unsigned int g_detBlockV = 32;
+// static const unsigned int g_anglesPerWeightBlock = 16;
+// static const unsigned int g_detBlockU = 32;
+// static const unsigned int g_detBlockV = 32;
 
 
 __global__ void devFDK_preweight(void* D_projData, unsigned int projPitch, unsigned int startAngle, unsigned int endAngle, float fSrcOrigin, float fDetOrigin, float fZShift, float fDetUSize, float fDetVSize, unsigned int iProjAngles, unsigned int iProjU, unsigned int iProjV)
 {
     float* projData = (float*)D_projData;
-    int angle = startAngle + blockIdx.y * g_anglesPerWeightBlock + threadIdx.y;
+
+    const uint angle = blockDim.y * blockIdx.y + threadIdx.y + startAngle;
+
     if (angle >= endAngle)
         return;
 
-    const int detectorU = (blockIdx.x%((iProjU+g_detBlockU-1)/g_detBlockU)) * g_detBlockU + threadIdx.x;
-    const int startDetectorV = (blockIdx.x/((iProjU+g_detBlockU-1)/g_detBlockU)) * g_detBlockV;
-    int endDetectorV = startDetectorV + g_detBlockV;
-    if (endDetectorV > iProjV)
-        endDetectorV = iProjV;
+    // Astra FDK kernel used this indexing (with the appropriate grid)
+    // const int detectorU = (blockIdx.x%((iProjU+g_detBlockU-1)/g_detBlockU)) * g_detBlockU + threadIdx.x;
+    // const int startDetectorV = (blockIdx.x/((iProjU+g_detBlockU-1)/g_detBlockU)) * g_detBlockV;
+    // Instead we choose a simpler scheme which does not assume pitch memory allocation
+
+    const uint detectorU = blockDim.x * blockIdx.x + threadIdx.x;
+    const int startDetectorV = 0;
+
+    int endDetectorV = iProjV; // startDetectorV + g_detBlockV;
+    // if (endDetectorV > iProjV)
+        // endDetectorV = iProjV;
+    if (detectorU >= iProjU) return;
+
 
     // We need the length of the central ray and the length of the ray(s) to
     // our detector pixel(s).

nabu/reconstruction/cone.py

@@ -1,10 +1,11 @@
+import logging
 from math import sqrt
 import numpy as np
 
 from ..cuda.kernel import CudaKernel
 from ..cuda.processing import CudaProcessing
 from ..reconstruction.filtering_cuda import CudaSinoFilter
-from ..utils import get_cuda_srcfile
+from ..utils import get_cuda_srcfile, updiv
 
 try:
     import astra
@@ -14,6 +15,9 @@ except ImportError:
     __have_astra__ = False
 
 
+_logger = logging.getLogger(__name__)
+
+
 class ConebeamReconstructor:
     """
     A reconstructor for cone-beam geometry using the astra toolbox.
@@ -159,7 +163,9 @@ class ConebeamReconstructor:
     def _init_fdk(self, padding_mode, filter_name):
         self.padding_mode = padding_mode
         self._use_astra_fdk = bool(self.extra_options.get("use_astra_fdk", True))
-        self._use_astra_fdk &= padding_mode in ["zeros", "constant", None, "none"]
+        if self._use_astra_fdk and padding_mode not in ["zeros", "constant", None, "none"]:
+            self._use_astra_fdk = False
+            _logger.warning("padding_mode was set to %s, cannot use native astra FDK" % padding_mode)
         if self._use_astra_fdk:
             return
         self.sino_filter = CudaSinoFilter(
@@ -386,12 +392,11 @@ def fdk_preweighting(d_sinos, proj_geom, relative_z_position=0.0, cor_shift=0.0)
         signature="Piiifffffiii",
     )
 
-    # n_angles, n_z, n_x = d_sinos.shape
     n_z, n_angles, n_x = d_sinos.shape
     det_origin = sqrt(proj_geom["DistanceOriginDetector"] ** 2 + cor_shift**2)
 
     block = (32, 16, 1)
-    grid = (((n_x + 32 - 1) // 32) * ((n_z + 32 - 1) // 32), (n_angles + 16 - 1) // 16, 1)
+    grid = (updiv(n_x, block[0]), updiv(n_angles, block[1]), 1)
 
     preweight_kernel(
         d_sinos,

nabu/reconstruction/tests/test_cone.py

@@ -1,7 +1,9 @@
+import logging
 import pytest
 import numpy as np
 from scipy.ndimage import gaussian_filter, shift
 from nabu.utils import subdivide_into_overlapping_segment, clip_circle
+from nabu.testutils import __do_long_tests__, generate_tests_scenarios
 
 try:
     import astra
@@ -387,6 +389,77 @@ class TestCone:
                 str(roi)
             )
 
+    def test_fdk_preweight(self, caplog):
+        """
+        Check that nabu's FDK pre-weighting give the same results as astra
+        """
+        shapes = [
+            {"n_z": 256, "n_x": 256, "n_a": 500},
+            # {"n_z": 250, "n_x": 340, "n_a": 250}, # Astra reconstruction is incorrect in this case!
+        ]
+        src_orig_dist = 1000
+        orig_det_dist = 50
+
+        rot_centers_from_middle = [0]
+        if __do_long_tests__:
+            rot_centers_from_middle.extend([10, -15])
+
+        params_list = generate_tests_scenarios({"shape": shapes, "rot_center": rot_centers_from_middle})
+
+        for params in params_list:
+            n_z = params["shape"]["n_z"]
+            n_x = n_y = params["shape"]["n_x"]
+            n_a = params["shape"]["n_a"]
+            rc = params["rot_center"]
+            volume, cone_data = generate_hollow_cube_cone_sinograms(
+                vol_shape=(n_z, n_y, n_x),
+                n_angles=n_a,
+                src_orig_dist=src_orig_dist,
+                orig_det_dist=orig_det_dist,
+                apply_filter=False,
+                rot_center_shift=rc,
+            )
+
+            reconstructor_args = [(n_z, n_a, n_x), src_orig_dist, orig_det_dist]
+            reconstructor_kwargs_base = {
+                "volume_shape": volume.shape,
+                "rot_center": (n_x - 1) / 2 + rc,
+                "cuda_options": {"ctx": self.ctx},
+            }
+            reconstructor_kwargs_astra = {"padding_mode": "zeros", "extra_options": {"use_astra_fdk": True}}
+            reconstructor_kwargs_nabu = {"padding_mode": "zeros", "extra_options": {"use_astra_fdk": False}}
+            reconstructor_astra = ConebeamReconstructor(
+                *reconstructor_args, **{**reconstructor_kwargs_base, **reconstructor_kwargs_astra}
+            )
+            assert reconstructor_astra._use_astra_fdk is True, "reconstructor_astra should use native astra FDK"
+            reconstructor_nabu = ConebeamReconstructor(
+                *reconstructor_args, **{**reconstructor_kwargs_base, **reconstructor_kwargs_nabu}
+            )
+            ref = reconstructor_astra.reconstruct(cone_data)
+            res = reconstructor_nabu.reconstruct(cone_data)
+
+            reconstructor_kwargs_nabu = {"padding_mode": "edges", "extra_options": {"use_astra_fdk": False}}
+            cb_ep = ConebeamReconstructor(
+                *reconstructor_args, **{**reconstructor_kwargs_base, **reconstructor_kwargs_nabu}
+            )
+            res_ep = cb_ep.reconstruct(cone_data)  # noqa: F841
+
+            assert np.max(np.abs(res - ref)) < 2e-3, "Wrong FDK results for parameters: %s" % (str(params))
+
+            # Test with edges padding - only nabu can do that
+            reconstructor_kwargs_nabu["padding_mode"] = "edges"
+            reconstructor_nabu = ConebeamReconstructor(
+                *reconstructor_args, **{**reconstructor_kwargs_base, **reconstructor_kwargs_nabu}
+            )
+            reconstructor_nabu.reconstruct(cone_data)
+            # result is slightly different than "res" in the borders, which is expected
+            # it would be good to test it as well, but it's outside of the scope of this test
+
+            with caplog.at_level(logging.WARNING):
+                reconstructor_kwargs_nabu = {"padding_mode": "edges", "extra_options": {"use_astra_fdk": True}}
+                ConebeamReconstructor(*reconstructor_args, **{**reconstructor_kwargs_base, **reconstructor_kwargs_nabu})
+                assert "cannot use native astra FDK" in caplog.text
+
 
 def generate_hollow_cube_cone_sinograms(
     vol_shape,
@@ -406,7 +479,7 @@ def generate_hollow_cube_cone_sinograms(
     prj_height = n_z
     angles = np.linspace(0, 2 * np.pi, n_angles, True)
 
-    proj_geom = astra.create_proj_geom("cone", 1.0, 1.0, prj_width, prj_width, angles, src_orig_dist, orig_det_dist)
+    proj_geom = astra.create_proj_geom("cone", 1.0, 1.0, n_z, prj_width, angles, src_orig_dist, orig_det_dist)
     if rot_center_shift is not None:
         proj_geom = astra.geom_postalignment(proj_geom, (-rot_center_shift, 0))
     magnification = 1 + orig_det_dist / src_orig_dist

{nabu-2024.2.4.dist-info → nabu-2024.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nabu
-Version: 2024.2.4
+Version: 2024.2.5
 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>
@@ -49,35 +49,35 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy <2,>1.9.0
+Requires-Dist: numpy<2,>1.9.0
 Requires-Dist: scipy
-Requires-Dist: h5py >=3.0
-Requires-Dist: silx >=0.15.0
-Requires-Dist: tomoscan >=2.1.0
+Requires-Dist: h5py>=3.0
+Requires-Dist: silx>=0.15.0
+Requires-Dist: tomoscan>=2.1.0
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile
 Requires-Dist: tqdm
-Provides-Extra: doc
-Requires-Dist: sphinx ; extra == 'doc'
-Requires-Dist: cloud-sptheme ; extra == 'doc'
-Requires-Dist: myst-parser ; extra == 'doc'
-Requires-Dist: nbsphinx ; extra == 'doc'
 Provides-Extra: full
-Requires-Dist: scikit-image ; extra == 'full'
-Requires-Dist: PyWavelets ; extra == 'full'
-Requires-Dist: glymur ; extra == 'full'
-Requires-Dist: pycuda !=2024.1.1 ; extra == 'full'
-Requires-Dist: scikit-cuda ; extra == 'full'
-Requires-Dist: pycudwt ; extra == 'full'
-Requires-Dist: sluurp >=0.3 ; extra == 'full'
-Requires-Dist: pyvkfft ; extra == 'full'
-Provides-Extra: full_nocuda
-Requires-Dist: scikit-image ; extra == 'full_nocuda'
-Requires-Dist: PyWavelets ; extra == 'full_nocuda'
-Requires-Dist: glymur ; extra == 'full_nocuda'
-Requires-Dist: sluurp >=0.3 ; extra == 'full_nocuda'
-Requires-Dist: pyvkfft ; extra == 'full_nocuda'
+Requires-Dist: scikit-image; extra == "full"
+Requires-Dist: PyWavelets; extra == "full"
+Requires-Dist: glymur; extra == "full"
+Requires-Dist: pycuda!=2024.1.1; extra == "full"
+Requires-Dist: scikit-cuda; extra == "full"
+Requires-Dist: pycudwt; extra == "full"
+Requires-Dist: sluurp>=0.3; extra == "full"
+Requires-Dist: pyvkfft; extra == "full"
+Provides-Extra: full-nocuda
+Requires-Dist: scikit-image; extra == "full-nocuda"
+Requires-Dist: PyWavelets; extra == "full-nocuda"
+Requires-Dist: glymur; extra == "full-nocuda"
+Requires-Dist: sluurp>=0.3; extra == "full-nocuda"
+Requires-Dist: pyvkfft; extra == "full-nocuda"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu
 

{nabu-2024.2.4.dist-info → nabu-2024.2.5.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=c6RQ-mRwrAgEkoyeON7u8FYClLvqty1oogHOSMgxIRw,270
+nabu/__init__.py,sha256=BhsllrJ2adOlOshSRwCN9w9DtOegccwzs8GPbrfvAUA,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -44,7 +44,7 @@ nabu/cuda/src/ElementOp.cu,sha256=PhebQQgeF0V7MDNzeYiRXIeNq3tE2PsBx00XhanBmvg,71
 nabu/cuda/src/backproj.cu,sha256=Zq9w8TP9zSYCHH_91dfrTVLOSEmY0y4hzm7J2qdCdJ8,6257
 nabu/cuda/src/backproj_polar.cu,sha256=sZbtw3KMfN69XyubJQSSLC87d5IPOyzbPBoRSNC1Cek,1851
 nabu/cuda/src/boundary.h,sha256=eQhfKZm-o0kj88BvkUwzqfqxYfRde4Tuj8AhQvRK16Y,2898
-nabu/cuda/src/cone.cu,sha256=Q-mKNBnx0pXzpOUGKi0Kq4POp7VqaQrLCDgqTf1pdkk,3071
+nabu/cuda/src/cone.cu,sha256=IuuVpHPnGekQmLq7_FyJ3pN4Ntjs7k5yeUiPKty7H9w,3399
 nabu/cuda/src/convolution.cu,sha256=O6r8qPpQjpaqnNivMRX0LK3dEACKk9xyNYO9u_JysU0,7353
 nabu/cuda/src/dfi_fftshift.cu,sha256=ElgNXy8H14mff2hmyjxCq7CnFK_DSY2Z564QGytRO1o,2220
 nabu/cuda/src/flatfield.cu,sha256=ZVVmEd-jcsK03VWv42uugYw6LeUnDEVY8qo_G07doHs,2058
@@ -220,7 +220,7 @@ nabu/processing/tests/test_rotation.py,sha256=vedRXV9RePJywBKoyBkGANP1dhZCjphbYO
 nabu/processing/tests/test_transpose.py,sha256=hTG17wTaB5Wv6twbW3ZFhBv6BYfqJY7DTQPoO0-KdkM,2760
 nabu/processing/tests/test_unsharp.py,sha256=R3ovbwDDp3ccy2A8t6CcUVELXRWkED5EnQdN2FQOfQM,4391
 nabu/reconstruction/__init__.py,sha256=EmKVvx_-FJvzJngG4ielIC7FhMCpI1Waaflg_lF44tk,163
-nabu/reconstruction/cone.py,sha256=WObFcHvv7NkaZhUoC_xTlvl95f38AjsAJkePSOzngVk,18870
+nabu/reconstruction/cone.py,sha256=RZj1JoxqskShvglgxUnsbYw7qbm6Rralt7hJ96eU-8c,19015
 nabu/reconstruction/fbp.py,sha256=uwEniGdEOn1atc9mTAHEDeF1y-ZqneifCKVr-ieHZss,5015
 nabu/reconstruction/fbp_base.py,sha256=DwZCilPXgGMRPV8_XfkWiaXUzWFM8rNBa8IyMdy5nno,17092
 nabu/reconstruction/fbp_opencl.py,sha256=coEGLq65PCuvWnhAbIyLPHACkWjMB0XOceMp9ZIDWtc,3274
@@ -238,7 +238,7 @@ nabu/reconstruction/sinogram.py,sha256=KTSGP_JJABf4Yr9l628HPbyWsBnpbnyGKyPEq3ZrP
 nabu/reconstruction/sinogram_cuda.py,sha256=DmTWdI9JhINjBpBuPiEt5mSqFmqu2FitIV94g3hSTAI,10659
 nabu/reconstruction/sinogram_opencl.py,sha256=vxJa5BeOd2NVdUayXYfQGAfO1AEbJfTGotuijT8qgCs,1486
 nabu/reconstruction/tests/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-nabu/reconstruction/tests/test_cone.py,sha256=2BsR1kHlnlronghckifGmcrtROWF43lilYo8TMDUTjo,17846
+nabu/reconstruction/tests/test_cone.py,sha256=Vb31LX_KXYU8FPlco9heFRHIftk0-RI5_LSbhX9OMIA,21453
 nabu/reconstruction/tests/test_deringer.py,sha256=XE97waf6TKFm-Kxe9PGQ-Vs_Pldn-OzvOolhuy7a5k4,8340
 nabu/reconstruction/tests/test_fbp.py,sha256=jj2eSRB56-xs4SM_pK3Q9EupKQWFTzbtraXPD165rcU,15291
 nabu/reconstruction/tests/test_filtering.py,sha256=I5H1KSfd4iXTJWSqeMPR5Q7v5rFTXO6Vp2jYU4ugl58,5247
@@ -310,9 +310,9 @@ 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-2024.2.4.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.4.dist-info/METADATA,sha256=8aKl-Zw_YMikzn33XIqdUzSbSqI4x3bUwhxL_wZi8Dc,5538
-nabu-2024.2.4.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
-nabu-2024.2.4.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.4.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.4.dist-info/RECORD,,
+nabu-2024.2.5.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.5.dist-info/METADATA,sha256=dagapyWNaPkQX79F5M8U6pRfmPJqczjoupUC41I5yfw,5514
+nabu-2024.2.5.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nabu-2024.2.5.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.5.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.5.dist-info/RECORD,,

{nabu-2024.2.4.dist-info → nabu-2024.2.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.1)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any