nabu 2024.2.0rc4__tar.gz → 2024.2.1__tar.gz

{nabu-2024.2.0rc4/nabu.egg-info → nabu-2024.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc4
+Version: 2024.2.1
 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>
@@ -48,36 +48,10 @@ 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
-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: 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"
+License-File: LICENSE
 
 # Nabu
 

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc4"
+__version__ = "2024.2.1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu/app/cli_configs.py

@@ -37,7 +37,7 @@ BootstrapConfig = {
         "default": "",
     },
     "template": {
-        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
+        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf, id16a_fluo, bm05_pag. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
         "default": "",
     },
     "helical": {"help": "Prepare configuration file for helical", "default": 0, "required": False, "type": int},

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu/pipeline/fullfield/processconfig.py

@@ -465,7 +465,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "chunk":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "chunk",
             }
@@ -513,7 +513,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "full":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "full",
             }

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu/pipeline/fullfield/reconstruction.py

@@ -253,7 +253,7 @@ class FullFieldReconstructor:
         if self.process_config.processing_options.get("phase", {}).get("method", None) == "CTF":
             force_grouped_mode = True
             msg = "CTF phase retrieval needs to process full radios"
-        if self.process_config.processing_options.get("tilt_correction", {}).get("angle", 0) > 15:
+        if (self.process_config.dataset_info.detector_tilt or 0) > 15:
             force_grouped_mode = True
             msg = "Radios rotation with a large angle needs to process full radios"
         if self.process_config.resume_from_step == "sinogram" and force_grouped_mode:

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu/resources/nxflatfield.py

@@ -35,12 +35,10 @@ def get_frame_possible_urls(dataset_info, user_dir, output_dir):
         else:
             dataurl_default_template = h5scan.REDUCED_DARKS_DATAURLS[0]
 
-        rel_file_path = dataurl_default_template.file_path().format(
-            scan_prefix=dataset_info.dataset_scanner.get_dataset_basename()
-        )
+        rel_file_path = dataurl_default_template.file_path().format(scan_prefix=h5scan.get_dataset_basename())
         return DataUrl(
             file_path=os.path.join(dirname, rel_file_path),
-            data_path=dataurl_default_template.data_path(),
+            data_path=dataurl_default_template.data_path().format(entry=h5scan.entry, index="{index}"),
             data_slice=dataurl_default_template.data_slice(),  # not sure if needed
             scheme="silx",
         )
@@ -144,9 +142,11 @@ def data_url_exists(data_url):
     """
     if not (os.path.isfile(data_url.file_path())):
         return False
+    group_exists = False
     with HDF5File(data_url.file_path(), "r") as f:
-        path_exists = f.get(data_url.data_path(), default=None) is not None
-    return path_exists
+        data_path_without_index = data_url.data_path().split("{")[0]
+        group_exists = f.get(data_path_without_index, default=None) is not None
+    return group_exists
 
 
 # pylint: disable=E1136

nabu-2024.2.1/nabu/resources/tests/test_extract.py

@@ -0,0 +1,10 @@
+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()

{nabu-2024.2.0rc4 → nabu-2024.2.1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc4
+Version: 2024.2.1
 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>
@@ -48,36 +48,10 @@ 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
-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: 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"
+License-File: LICENSE
 
 # Nabu
 

{nabu-2024.2.0rc4 → nabu-2024.2.1}/nabu.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ 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
@@ -41,6 +40,7 @@ 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
@@ -230,7 +230,6 @@ 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
@@ -273,6 +272,7 @@ 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-2024.2.0rc4 → nabu-2024.2.1}/nabu.egg-info/top_level.txt

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

nabu-2024.2.0rc4/doc/doc_config.py

@@ -1,32 +0,0 @@
-#!/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-2024.2.0rc4/nabu/reconstruction/astra.py

@@ -1,244 +0,0 @@
-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)