nabu 2024.2.7__py3-none-any.whl → 2024.2.8__py3-none-any.whl

doc/doc_config.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+from nabu.resources.nabu_config import nabu_config
+
+
+def generate(file_):
+    def write(content):
+        print(content, file=file_)
+    for section, values in nabu_config.items():
+        if section == "about":
+            continue
+        write("## %s\n" % section)
+        for key, val in values.items():
+            if val["type"] == "unsupported":
+                continue
+            write(val["help"] + "\n")
+            write(
+                "```ini\n%s = %s\n```"
+                % (key, val["default"])
+            )
+
+
+
+if __name__ == "__main__":
+
+    import sys, os
+    print(os.path.abspath(__file__))
+    exit(0)
+
+    fname = "/tmp/test.md"
+    with open(fname, "w") as f:
+        generate(f)

nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.7"
+__version__ = "2024.2.8"
 __nabu_modules__ = [
     "app",
     "cuda",

nabu/pipeline/estimators.py

@@ -150,7 +150,7 @@ class CORFinderBase:
                 lookup_side = default_lookup_side
             else:
                 lookup_side = initial_cor_pos
-            self._lookup_side = initial_cor_pos
+            self._lookup_side = lookup_side
 
     def _init_cor_finder(self):
         cor_finder_cls = self.search_methods[self.method]["class"]

nabu/pipeline/fullfield/nabu_config.py

@@ -15,7 +15,7 @@ nabu_config = {
             "type": "advanced",
         },
         "nexus_version": {
-            "default": "1.0",
+            "default": "1.4",
             "help": "Nexus version to use when browsing the HDF5 dataset. Default is 1.0.",
             "validator": float_validator,
             "type": "advanced",

nabu/reconstruction/astra.py

@@ -0,0 +1,245 @@
+# ruff: noqa
+try:
+    import astra
+
+    __have_astra__ = True
+except ImportError:
+    __have_astra__ = False
+    astra = None
+
+
+class AstraReconstructor:
+    """
+    Base class for reconstructors based on the Astra toolbox
+    """
+
+    default_extra_options = {
+        "axis_correction": None,
+        "clip_outer_circle": False,
+        "scale_factor": None,
+        "filter_cutoff": 1.0,
+        "outer_circle_value": 0.0,
+    }
+
+    def __init__(
+        self,
+        sinos_shape,
+        angles=None,
+        volume_shape=None,
+        rot_center=None,
+        pixel_size=None,
+        padding_mode="zeros",
+        filter_name=None,
+        slice_roi=None,
+        cuda_options=None,
+        extra_options=None,
+    ):
+        self._configure_extra_options(extra_options)
+        self._init_cuda(cuda_options)
+        self._set_sino_shape(sinos_shape)
+        self._orig_prog_geom = None
+        self._init_geometry(
+            source_origin_dist,
+            origin_detector_dist,
+            pixel_size,
+            angles,
+            volume_shape,
+            rot_center,
+            relative_z_position,
+            slice_roi,
+        )
+        self._init_fdk(padding_mode, filter_name)
+        self._alg_id = None
+        self._vol_id = None
+        self._proj_id = None
+
+    def _configure_extra_options(self, extra_options):
+        self.extra_options = self.default_extra_options.copy()
+        self.extra_options.update(extra_options or {})
+
+    def _init_cuda(self, cuda_options):
+        cuda_options = cuda_options or {}
+        self.cuda = CudaProcessing(**cuda_options)
+
+    def _set_sino_shape(self, sinos_shape):
+        if len(sinos_shape) != 3:
+            raise ValueError("Expected a 3D shape")
+        self.sinos_shape = sinos_shape
+        self.n_sinos, self.n_angles, self.prj_width = sinos_shape
+
+    def _set_pixel_size(self, pixel_size):
+        if pixel_size is None:
+            det_spacing_y = det_spacing_x = 1
+        elif np.iterable(pixel_size):
+            det_spacing_y, det_spacing_x = pixel_size
+        else:
+            # assuming scalar
+            det_spacing_y = det_spacing_x = pixel_size
+        self._det_spacing_y = det_spacing_y
+        self._det_spacing_x = det_spacing_x
+
+    def _set_slice_roi(self, slice_roi):
+        self.slice_roi = slice_roi
+        self._vol_geom_n_x = self.n_x
+        self._vol_geom_n_y = self.n_y
+        self._crop_data = True
+        if slice_roi is None:
+            return
+        start_x, end_x, start_y, end_y = slice_roi
+        if roi_is_centered(self.volume_shape[1:], (slice(start_y, end_y), slice(start_x, end_x))):
+            # Astra can only reconstruct subregion centered around the origin
+            self._vol_geom_n_x = self.n_x - start_x * 2
+            self._vol_geom_n_y = self.n_y - start_y * 2
+        else:
+            raise NotImplementedError(
+                "Astra supports only slice_roi centered around origin (got slice_roi=%s with n_x=%d, n_y=%d)"
+                % (str(slice_roi), self.n_x, self.n_y)
+            )
+
+    def _init_geometry(
+        self,
+        source_origin_dist,
+        origin_detector_dist,
+        pixel_size,
+        angles,
+        volume_shape,
+        rot_center,
+        relative_z_position,
+        slice_roi,
+    ):
+        if angles is None:
+            self.angles = np.linspace(0, 2 * np.pi, self.n_angles, endpoint=True)
+        else:
+            self.angles = angles
+        if volume_shape is None:
+            volume_shape = (self.sinos_shape[0], self.sinos_shape[2], self.sinos_shape[2])
+        self.volume_shape = volume_shape
+        self.n_z, self.n_y, self.n_x = self.volume_shape
+        self.source_origin_dist = source_origin_dist
+        self.origin_detector_dist = origin_detector_dist
+        self.magnification = 1 + origin_detector_dist / source_origin_dist
+        self._set_slice_roi(slice_roi)
+        self.vol_geom = astra.create_vol_geom(self._vol_geom_n_y, self._vol_geom_n_x, self.n_z)
+        self.vol_shape = astra.geom_size(self.vol_geom)
+        self._cor_shift = 0.0
+        self.rot_center = rot_center
+        if rot_center is not None:
+            self._cor_shift = (self.sinos_shape[-1] - 1) / 2.0 - rot_center
+        self._set_pixel_size(pixel_size)
+        self._axis_corrections = self.extra_options.get("axis_correction", None)
+        self._create_astra_proj_geometry(relative_z_position)
+
+    def _create_astra_proj_geometry(self, relative_z_position):
+        # This object has to be re-created each time, because once the modifications below are done,
+        # it is no more a "cone" geometry but a "cone_vec" geometry, and cannot be updated subsequently
+        # (see astra/functions.py:271)
+        self.proj_geom = astra.create_proj_geom(
+            "cone",
+            self._det_spacing_x,
+            self._det_spacing_y,
+            self.n_sinos,
+            self.prj_width,
+            self.angles,
+            self.source_origin_dist,
+            self.origin_detector_dist,
+        )
+        self.relative_z_position = relative_z_position or 0.0
+        # This will turn the geometry of type "cone" into a geometry of type "cone_vec"
+        if self._orig_prog_geom is None:
+            self._orig_prog_geom = self.proj_geom
+        self.proj_geom = astra.geom_postalignment(self.proj_geom, (self._cor_shift, 0))
+        # (src, detector_center, u, v) = (srcX, srcY, srcZ, dX, dY, dZ, uX, uY, uZ, vX, vY, vZ)
+        vecs = self.proj_geom["Vectors"]
+
+        # To adapt the center of rotation:
+        # dX = cor_shift * cos(theta) - origin_detector_dist * sin(theta)
+        # dY = origin_detector_dist * cos(theta) + cor_shift * sin(theta)
+        if self._axis_corrections is not None:
+            # should we check that dX and dY match the above formulas ?
+            cor_shifts = self._cor_shift + self._axis_corrections
+            vecs[:, 3] = cor_shifts * np.cos(self.angles) - self.origin_detector_dist * np.sin(self.angles)
+            vecs[:, 4] = self.origin_detector_dist * np.cos(self.angles) + cor_shifts * np.sin(self.angles)
+
+        # To adapt the z position:
+        # Component 2 of vecs is the z coordinate of the source, component 5 is the z component of the detector position
+        # We need to re-create the same inclination of the cone beam, thus we need to keep the inclination of the two z positions.
+        # The detector is centered on the rotation axis, thus moving it up or down, just moves it out of the reconstruction volume.
+        # We can bring back the detector in the correct volume position, by applying a rigid translation of both the detector and the source.
+        # The translation is exactly the amount that brought the detector up or down, but in the opposite direction.
+        vecs[:, 2] = -self.relative_z_position
+
+    def _set_output(self, volume):
+        if volume is not None:
+            expected_shape = self.vol_shape  # if not (self._crop_data) else self._output_cropped_shape
+            self.cuda.check_array(volume, expected_shape)
+            self.cuda.set_array("output", volume)
+        if volume is None:
+            self.cuda.allocate_array("output", self.vol_shape)
+        d_volume = self.cuda.get_array("output")
+        z, y, x = d_volume.shape
+        self._vol_link = astra.data3d.GPULink(d_volume.ptr, x, y, z, d_volume.strides[-2])
+        self._vol_id = astra.data3d.link("-vol", self.vol_geom, self._vol_link)
+
+    def _set_input(self, sinos):
+        self.cuda.check_array(sinos, self.sinos_shape)
+        self.cuda.set_array("sinos", sinos)  # self.cuda.sinos is now a GPU array
+        # TODO don't create new link/proj_id if ptr is the same ?
+        # But it seems Astra modifies the input sinogram while doing FDK, so this might be not relevant
+        d_sinos = self.cuda.get_array("sinos")
+
+        # self._proj_data_link = astra.data3d.GPULink(d_sinos.ptr, self.prj_width, self.n_angles, self.n_z, sinos.strides[-2])
+        self._proj_data_link = astra.data3d.GPULink(
+            d_sinos.ptr, self.prj_width, self.n_angles, self.n_sinos, d_sinos.strides[-2]
+        )
+        self._proj_id = astra.data3d.link("-sino", self.proj_geom, self._proj_data_link)
+
+    def _preprocess_data(self):
+        d_sinos = self.cuda.sinos
+        for i in range(d_sinos.shape[0]):
+            self.sino_filter.filter_sino(d_sinos[i], output=d_sinos[i])
+
+    def _update_reconstruction(self):
+        cfg = astra.astra_dict("BP3D_CUDA")
+        cfg["ReconstructionDataId"] = self._vol_id
+        cfg["ProjectionDataId"] = self._proj_id
+        if self._alg_id is not None:
+            astra.algorithm.delete(self._alg_id)
+        self._alg_id = astra.algorithm.create(cfg)
+
+    def reconstruct(self, sinos, output=None, relative_z_position=None):
+        """
+        sinos: numpy.ndarray or pycuda.gpuarray
+            Sinograms, with shape (n_sinograms, n_angles, width)
+        output: pycuda.gpuarray, optional
+            Output array. If not provided, a new numpy array is returned
+        relative_z_position: int, optional
+            Position of the central slice of the slab, with respect to the full stack of slices.
+            By default it is set to zero, meaning that the current slab is assumed in the middle of the stack
+        """
+        self._create_astra_proj_geometry(relative_z_position)
+        self._set_input(sinos)
+        self._set_output(output)
+        self._preprocess_data()
+        self._update_reconstruction()
+        astra.algorithm.run(self._alg_id)
+        #
+        # NB: Could also be done with
+        # from astra.experimental import direct_BP3D
+        # projector_id = astra.create_projector("cuda3d", self.proj_geom, self.vol_geom, options=None)
+        # direct_BP3D(projector_id, self._vol_link, self._proj_data_link)
+        #
+        result = self.cuda.get_array("output")
+        if output is None:
+            result = result.get()
+        if self.extra_options.get("scale_factor", None) is not None:
+            result *= np.float32(self.extra_options["scale_factor"])  # in-place for pycuda
+        self.cuda.recover_arrays_references(["sinos", "output"])
+        return result
+
+    def __del__(self):
+        if getattr(self, "_alg_id", None) is not None:
+            astra.algorithm.delete(self._alg_id)
+        if getattr(self, "_vol_id", None) is not None:
+            astra.data3d.delete(self._vol_id)
+        if getattr(self, "_proj_id", None) is not None:
+            astra.data3d.delete(self._proj_id)

{nabu-2024.2.7.dist-info → nabu-2024.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nabu
-Version: 2024.2.7
+Version: 2024.2.8
 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-2024.2.7.dist-info → nabu-2024.2.8.dist-info}/RECORD

@@ -1,7 +1,8 @@
 doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
 doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
+doc/doc_config.py,sha256=anqeOVjqE2e7eVzg7yuh9dvIneTkrA5doGl1cVBqT7Q,730
 doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
-nabu/__init__.py,sha256=jfYqwDZB9SZV1cW-GiBKmgxrQpKNF9PxVpFn-1m65Yg,270
+nabu/__init__.py,sha256=zSq-gJem_m5BV0pkafmuCesRi5_d0UbEMfnIUh2eStg,270
 nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
 nabu/testutils.py,sha256=VkSL9tbY0XEH49Z5OjDFFhzkSxrCv4UIuvSVFgegSUY,7632
 nabu/utils.py,sha256=V1B_sD54XGNKn5pORa2yNCATyswOzybey3sv8BuIYWY,26355
@@ -130,7 +131,7 @@ nabu/pipeline/config_validators.py,sha256=ocAKB26iRjm5qs1Ay4B_rgGcg8aZjAP34XpEZR
 nabu/pipeline/datadump.py,sha256=lK36YlsVSeE4fdkD7cgVCl4RKn-Wa9KYgOw4DNtH8Ow,6982
 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=QfjExqNPKON3dsHmkEboXBA18ierlHhx-VIBe2m7Otk,40473
+nabu/pipeline/estimators.py,sha256=ME5o6Tzoi6_qFplLOS7LkN9DPouBAqpoIQAcK7SbWB0,40469
 nabu/pipeline/params.py,sha256=EoovjCUTUXmj5HQ3qE0RhP7XD3cndaiT21TdvjTIhE8,3746
 nabu/pipeline/processconfig.py,sha256=3xx2Lc8uEzPAqSMwUncr4RCiCtKn2c7wnXXbPSn8GNo,7719
 nabu/pipeline/reader.py,sha256=wkxPHYOi_C8dHNc7kddB8AMtFuW7GjsP_tm6SJeHlEY,4792
@@ -141,7 +142,7 @@ nabu/pipeline/fullfield/chunked.py,sha256=6fHkofoFcCEYbdowCJU7s7c-hPaM62qv8PGSV_
 nabu/pipeline/fullfield/chunked_cuda.py,sha256=Jdkk6ZIt3S6UZYbupHtSj2vrj3krWMcqRHHprfblDfk,5848
 nabu/pipeline/fullfield/computations.py,sha256=AEp3qvwyY-l8-GzjH1E6kmcmU6OgDp6sB-mltq0Jnxg,9970
 nabu/pipeline/fullfield/dataset_validator.py,sha256=Iy6oOnXnBldDcg0ifm_zzrzMQ6YdkR_hkHFySZgxbno,2943
-nabu/pipeline/fullfield/nabu_config.py,sha256=rvHmCNHx2y-GKBidRWCAjJd0IynvolPTTmBqNoOSvEA,31877
+nabu/pipeline/fullfield/nabu_config.py,sha256=E67oAzRY2YlE6VWZPOS-0WDk-z_cu4UMLgHqPZSjUHY,31877
 nabu/pipeline/fullfield/processconfig.py,sha256=2eE9W0KjsHq8aSCXlczsISpWM9SMjWL03fN1RqZWyxg,36815
 nabu/pipeline/fullfield/reconstruction.py,sha256=LpIMyl8LLJoJLhayHXT3VyOwRpEL9tdjPhIegFUS388,37678
 nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -220,6 +221,7 @@ 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/astra.py,sha256=qnFYabU-Bzgys8hXjIBcwO2NazrvhNXUYFIkMHc6BmM,10444
 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
@@ -309,9 +311,9 @@ 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-2024.2.7.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
-nabu-2024.2.7.dist-info/METADATA,sha256=KhmcCqJFd0DXEKQ3YP42BSC5a7yedWK1Cx0VLsukF9s,5514
-nabu-2024.2.7.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nabu-2024.2.7.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
-nabu-2024.2.7.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
-nabu-2024.2.7.dist-info/RECORD,,
+nabu-2024.2.8.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.2.8.dist-info/METADATA,sha256=5JnlQzXe6xXuHXklw49GyMS08SUq1hiIPSTUhG6jbiw,5514
+nabu-2024.2.8.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nabu-2024.2.8.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.2.8.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.2.8.dist-info/RECORD,,