nabu 2024.2.0rc3__tar.gz → 2024.2.0rc4__tar.gz

{nabu-2024.2.0rc3/nabu.egg-info → nabu-2024.2.0rc4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc3
+Version: 2024.2.0rc4
 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>
@@ -48,10 +48,36 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 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: scipy
+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: full
-Provides-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
-License-File: LICENSE
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu
 

nabu-2024.2.0rc4/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-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc3"
+__version__ = "2024.2.0-rc4"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/estimation/cor.py

@@ -239,7 +239,7 @@ class CenterOfRotationSlidingWindow(CenterOfRotation):
                 win_2_start = img_width // 2 - window_shift
         else:
             abs_pos = int(side + img_width // 2)
-            window_fraction = 0.2  # Hard-coded ?
+            window_fraction = 0.1  # Hard-coded ?
 
             window_width = round(window_fraction * img_width)
             window_shift = window_width // 2

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/pipeline/estimators.py

@@ -243,13 +243,13 @@ class CORFinder(CORFinderBase):
         # All find_shift() methods in self.search_methods have the same API with "img_1" and "img_2"
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
-        # FIXME
+        # ----- FIXME -----
         # 'self.cor_options' can contain 'side="from_file"', and we should not modify it directly
         # because it's entered by the user.
         # Either make a copy of self.cor_options, or change the inspect() mechanism
-        if cor_exec_kwargs["side"] == "from_file":
+        if cor_exec_kwargs.get("side", None) == "from_file":
             cor_exec_kwargs["side"] = self._lookup_side or "center"
-        #
+        # ------
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
         self.logger.debug("%s.find_shift(%s)" % (self.cor_finder.__class__.__name__, str(cor_exec_kwargs)))

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/pipeline/fullfield/chunked.py

@@ -668,7 +668,10 @@ class ChunkedPipeline:
             "jpeg2000_compression_ratio": options["jpeg2000_compression_ratio"],
             "float_clip_values": options["float_clip_values"],
             "tiff_single_file": options.get("tiff_single_file", False),
-            "single_output_file_initialized": getattr(self.process_config, "single_output_file_initialized", False),
+            "single_output_file_initialized": getattr(
+                self.process_config, "single_output_file_initialized", False
+            ),  # COMPAT.
+            "writer_initialized": getattr(self.process_config, "_writer_initialized", False),
             "raw_vol_metadata": {"voxelSize": self.dataset_info.pixel_size},  # legacy...
         }
         writer_extra_options.update(extra_options)
@@ -853,7 +856,8 @@ class ChunkedPipeline:
         self.writer.write_data(data)
         self.logger.info("Wrote %s" % self.writer.fname)
         self._write_histogram()
-        self.process_config.single_output_file_initialized = True
+        self.process_config.single_output_file_initialized = True  # COMPAT.
+        self.process_config._writer_initialized = True
 
     def _write_histogram(self):
         if "histogram" not in self.processing_steps:

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/pipeline/writer.py

@@ -1,5 +1,6 @@
 from os import path
 from tomoscan.esrf import TIFFVolume, MultiTIFFVolume, EDFVolume, JP2KVolume
+from tomoscan.esrf.volume.singleframebase import VolumeSingleFrameBase
 from ..utils import check_supported, get_num_threads
 from ..resources.logger import LoggerOrPrint
 from ..io.writer import NXProcessWriter, HSTVolVolume, NXVolVolume
@@ -113,6 +114,7 @@ class WriterManager:
         return vol_writer.data_url.file_path()
 
     def _init_writer(self):
+        self._writer_was_already_initialized = self.extra_options.get("writer_initialized", False)
         if self.file_format in ["tiff", "edf", "jp2", "hdf5"]:
             writer_kwargs = {
                 "folder": self.output_dir,
@@ -143,6 +145,11 @@ class WriterManager:
         self._h5_entry = self.metadata.get("entry", "entry")
         self.writer = self._writer_classes[self.file_format](**writer_kwargs)
         self.fname = self.get_fname(self.writer)
+        # In certain cases, tomoscan needs to remove any previous existing volume filess
+        # and avoid calling 'clean_output_data' when writing downstream (for chunk processing)
+        if isinstance(self.writer, VolumeSingleFrameBase):
+            self.writer.skip_existing_data_files_removal = self._writer_was_already_initialized
+        # ---
         if path.exists(self.fname):
             err = "File already exists: %s" % self.fname
             if self.overwrite:

nabu-2024.2.0rc4/nabu/reconstruction/astra.py

@@ -0,0 +1,244 @@
+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-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu/resources/dataset_analyzer.py

@@ -52,7 +52,7 @@ class DatasetAnalyzer:
             "output_dir": None,
             "exclude_projections": None,
             "hdf5_entry": None,
-            "nx_version": 1.0,
+            # "nx_version": 1.0,
         }
         # --
         advanced_options.update(extra_options)

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc3
+Version: 2024.2.0rc4
 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>
@@ -48,10 +48,36 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 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: scipy
+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: full
-Provides-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
-License-File: LICENSE
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu
 

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ README.md
 pyproject.toml
 doc/conf.py
 doc/create_conf_doc.py
+doc/doc_config.py
 doc/get_mathjax.py
 nabu/__init__.py
 nabu/tests.py
@@ -40,7 +41,6 @@ nabu/app/shrink_dataset.py
 nabu/app/stitching.py
 nabu/app/utils.py
 nabu/app/validator.py
-nabu/app/tests/__init__.py
 nabu/app/tests/test_reduce_dark_flat.py
 nabu/cuda/__init__.py
 nabu/cuda/convolution.py
@@ -230,6 +230,7 @@ nabu/processing/tests/test_rotation.py
 nabu/processing/tests/test_transpose.py
 nabu/processing/tests/test_unsharp.py
 nabu/reconstruction/__init__.py
+nabu/reconstruction/astra.py
 nabu/reconstruction/cone.py
 nabu/reconstruction/fbp.py
 nabu/reconstruction/fbp_base.py
@@ -272,7 +273,6 @@ nabu/resources/templates/id16_holo.conf
 nabu/resources/templates/id16a_fluo.conf
 nabu/resources/templates/id19_pag.conf
 nabu/resources/tests/__init__.py
-nabu/resources/tests/test_extract.py
 nabu/resources/tests/test_nxflatfield.py
 nabu/resources/tests/test_units.py
 nabu/stitching/__init__.py

{nabu-2024.2.0rc3 → nabu-2024.2.0rc4}/nabu.egg-info/top_level.txt

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

nabu-2024.2.0rc3/nabu/resources/tests/test_extract.py

@@ -1,10 +0,0 @@
-import pytest
-from nabu.utils import list_match_queries
-
-
-def test_list_match_queries():
-
-    # entry0000 .... entry0099
-    avail = ["entry%04d" % i for i in range(100)]
-    query = "entry0000"
-    list_match_queries()