nabu 2024.2.13__py3-none-any.whl → 2025.1.0__py3-none-any.whl

nabu-2025.1.0.dist-info/RECORD

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+nabu-2025.1.0.dist-info/RECORD,,

{nabu-2024.2.13.dist-info → nabu-2025.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{nabu-2024.2.13.dist-info → nabu-2025.1.0.dist-info}/entry_points.txt

@@ -8,12 +8,13 @@ nabu-diag2pix = nabu.app.diag_to_pix:main
 nabu-diag2rot = nabu.app.diag_to_rot:main
 nabu-display-timings = nabu.app.parse_reconstruction_log:parse_reclog_cli
 nabu-double-flatfield = nabu.app.double_flatfield:dff_cli
+nabu-estimate-motion = nabu.app.estimate_motion:estimate_motion
 nabu-generate-info = nabu.app.generate_header:generate_merged_info_file
 nabu-helical = nabu.app.reconstruct_helical:main_helical
-nabu-helical-correct-rot = nabu.app.correct_rot:main
 nabu-helical-prepare-weights-double = nabu.app.prepare_weights_double:main
 nabu-histogram = nabu.app.histogram:histogram_cli
 nabu-multicor = nabu.app.multicor:main
+nabu-pcaflats = nabu.app.pcaflats:main
 nabu-poly2map = nabu.app.create_distortion_map_from_poly:create_distortion_maps_entry_point
 nabu-reduce-dark-flat = nabu.app.reduce_dark_flat:main
 nabu-rotate = nabu.app.rotate:rotate_cli

nabu/app/correct_rot.py

@@ -1,70 +0,0 @@
-from .. import version
-from os import environ
-
-import argparse
-import shutil
-import os
-import sys
-import re
-import h5py
-import numpy as np
-
-
-from ..resources.logger import LoggerOrPrint
-from .utils import parse_params_values
-from .cli_configs import CorrectRotConfig
-from silx.io.dictdump import h5todict
-
-from nxtomo.application.nxtomo import NXtomo
-
-import h5py
-from nabu.utils import DictToObj
-
-
-def main(user_args=None):
-    """Applies the correction found by diag_to_rot to a nexus file"""
-
-    if user_args is None:
-        user_args = sys.argv[1:]
-
-    args = DictToObj(
-        parse_params_values(
-            CorrectRotConfig,
-            parser_description=main.__doc__,
-            program_version="nabu " + version,
-            user_args=user_args,
-        )
-    )
-
-    # now we read the results of the diag_to_rot utility, they are in the cor_file parameter
-    # of the cli
-    cor_data = DictToObj(h5todict(args.cor_file, "/"))
-
-    my_cor = cor_data.cor[0]
-    # we will take my_cor as cor at the first angular position
-    # and then we correct the x_translation at the other angles
-
-    # We now load the nexus that we wish to correct
-    nx_tomo = NXtomo().load(args.nexus_source, args.entry_name)
-
-    # The cor_file that we use for correction
-    # is providing us with the z_m that gives for each
-    # cor position found in the cor array the corresponding value of
-    # the translation along z (in meters)
-    z_translation = nx_tomo.sample.z_translation.value
-    z_translation = z_translation - z_translation[0]
-
-    # now we interpolate to find the correction
-    # for each position of the encoders
-    cors = np.interp(z_translation, cor_data.z_m, cor_data.cor)
-
-    # this is the correction
-    x_correction = nx_tomo.instrument.detector.x_pixel_size.value * (cors - my_cor)  # we are in meters here
-
-    # and we apply it to the nexus that we have loaded
-    nx_tomo.sample.x_translation = nx_tomo.sample.x_translation.value + x_correction
-
-    # finally we write it to the corrected nexus file
-    nx_tomo.save(file_path=args.nexus_target, data_path=args.entry_name, overwrite=True)
-
-    return 0

nabu/io/tests/test_detector_distortion.py

@@ -1,178 +0,0 @@
-import pytest
-import numpy as np
-import scipy.ndimage
-from scipy import sparse
-from nabu.io.detector_distortion import DetectorDistortionBase
-from nabu.processing.rotation import Rotation, __have__skimage__
-
-if __have__skimage__:
-    import skimage
-
-
-@pytest.mark.skipif(not (__have__skimage__), reason="Need scikit-image for rotation")
-def test_detector_distortion():
-    image = scipy.ndimage.gaussian_filter(np.random.random([379, 1357]), 3.0)
-    center_xz = ((image.shape[1] - 1) / 2, (image.shape[0] - 1) / 2)
-
-    part_to_be_retrieved = image[100:279]
-
-    rotated_image = skimage.transform.rotate(image, angle=5.0, center=center_xz[::])
-
-    corrector = DetectorDistortionRotation(detector_full_shape_vh=image.shape, center_xz=center_xz, angle_deg=-5.0)
-    start_x, end_x, start_z, end_z = corrector.set_sub_region_transformation(
-        target_sub_region=(
-            None,
-            None,
-            100,
-            279,
-        )
-    )
-
-    source = rotated_image[start_z:end_z, start_x:end_x]
-
-    retrieved = corrector.transform(source)
-
-    diff = (retrieved - part_to_be_retrieved)[:, 20:-20]
-
-    assert abs(diff).std() < 1e-3
-
-
-class DetectorDistortionRotation(DetectorDistortionBase):
-    """ """
-
-    def __init__(self, detector_full_shape_vh=(0, 0), center_xz=(0, 0), angle_deg=0.0):
-        """This is the basis class.
-        A simple identity transformation which has the only merit to show
-        how it works.Reimplement this function to have more parameters for other
-        transformations
-        """
-        self._build_full_transformation(detector_full_shape_vh, center_xz, angle_deg)
-
-    def _build_full_transformation(self, detector_full_shape_vh, center_xz, angle_deg):
-        """A simple identity.
-        Reimplement this function to have more parameters for other
-        transformations
-        """
-
-        indices = np.indices(detector_full_shape_vh)
-        center_x, center_z = center_xz
-        coordinates = (indices.T - np.array([center_z, center_x])).T
-
-        c = np.cos(np.deg2rad(angle_deg))
-        s = np.sin(np.deg2rad(angle_deg))
-
-        rot_mat = np.array([[c, s], [-s, c]])
-
-        coordinates = np.tensordot(rot_mat, coordinates, axes=[1, 0])
-
-        # padding
-        sz, sx = detector_full_shape_vh
-        total_detector_npixs = sz * sx
-        xs = np.clip(np.array(coordinates[1].flat) + center_x, [[0]], [[sx - 1]])
-        zs = np.clip(np.array(coordinates[0].flat) + center_z, [[0]], [[sz - 1]])
-
-        ix0s = np.floor(xs)
-        ix1s = np.ceil(xs)
-        fx = xs - ix0s
-
-        iz0s = np.floor(zs)
-        iz1s = np.ceil(zs)
-        fz = zs - iz0s
-
-        I_tmp = np.empty([4 * sz * sx], np.int64)
-        J_tmp = np.empty([4 * sz * sx], np.int64)
-        V_tmp = np.ones([4 * sz * sx], "f")
-
-        I_tmp[:] = np.arange(sz * sx * 4) // 4
-
-        J_tmp[0::4] = iz0s * sx + ix0s
-        J_tmp[1::4] = iz0s * sx + ix1s
-        J_tmp[2::4] = iz1s * sx + ix0s
-        J_tmp[3::4] = iz1s * sx + ix1s
-
-        V_tmp[0::4] = (1 - fz) * (1 - fx)
-        V_tmp[1::4] = (1 - fz) * fx
-        V_tmp[2::4] = fz * (1 - fx)
-        V_tmp[3::4] = fz * fx
-
-        self.detector_full_shape_vh = detector_full_shape_vh
-
-        coo_tmp = sparse.coo_matrix((V_tmp.astype("f"), (I_tmp, J_tmp)), shape=(sz * sx, sz * sx))
-
-        csr_tmp = coo_tmp.tocsr()
-
-        self.full_csr_data = csr_tmp.data
-        self.full_csr_indices = csr_tmp.indices
-        self.full_csr_indptr = csr_tmp.indptr
-
-        ## This will be used to save time if the same sub_region argument is requested several time in a row
-        self._status = None
-
-    def _set_sub_region_transformation(
-        self,
-        target_sub_region=(
-            (
-                None,
-                None,
-                0,
-                0,
-            ),
-        ),
-    ):
-        (x_start, x_end, z_start, z_end) = target_sub_region
-
-        if z_start is None:
-            z_start = 0
-        if z_end is None:
-            z_end = self.detector_full_shape_vh[0]
-
-        if (x_start, x_end) not in [(None, None), (0, None), (0, self.detector_full_shape_vh[1])]:
-            message = f""" In the base class DetectorDistortionRotation only vertical slicing is accepted.
-            The sub_region contained (x_start, x_end)={(x_start, x_end)} which would slice the 
-            full horizontal size which is {self.detector_full_shape_vh[1]}
-            """
-            raise ValueError()
-
-        x_start, x_end = 0, self.detector_full_shape_vh[1]
-
-        row_ptr_start = z_start * self.detector_full_shape_vh[1]
-        row_ptr_end = z_end * self.detector_full_shape_vh[1]
-
-        indices_start = self.full_csr_indptr[row_ptr_start]
-        indices_end = self.full_csr_indptr[row_ptr_end]
-
-        data_tmp = self.full_csr_data[indices_start:indices_end]
-
-        target_offset = self.full_csr_indptr[row_ptr_start]
-        indptr_tmp = self.full_csr_indptr[row_ptr_start : row_ptr_end + 1] - target_offset
-
-        indices_tmp = self.full_csr_indices[indices_start:indices_end]
-
-        iz_source = (indices_tmp) // self.detector_full_shape_vh[1]
-
-        z_start_source = iz_source.min()
-        z_end_source = iz_source.max() + 1
-        source_offset = z_start_source * self.detector_full_shape_vh[1]
-        indices_tmp = indices_tmp - source_offset
-
-        target_size = (z_end - z_start) * self.detector_full_shape_vh[1]
-        source_size = (z_end_source - z_start_source) * self.detector_full_shape_vh[1]
-
-        self.transformation_matrix = sparse.csr_matrix(
-            (data_tmp, indices_tmp, indptr_tmp), shape=(target_size, source_size)
-        )
-
-        self.target_shape = ((z_end - z_start), self.detector_full_shape_vh[1])
-
-        ## For the identity matrix the source and the target have the same size.
-        ## The two following lines are trivial.
-        ## For this identity transformation only the slicing of the appropriate part
-        ## of the identity sparse matrix is slightly laborious.
-        ## Practical case will be more complicated and source_sub_region
-        ## will be in general larger than the target_sub_region
-        self._status = {
-            "target_sub_region": ((x_start, x_end, z_start, z_end)),
-            "source_sub_region": ((x_start, x_end, z_start_source, z_end_source)),
-        }
-
-        return self._status["source_sub_region"]