nabu 2024.1.2__py3-none-any.whl → 2024.1.4__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- doc/doc_config.py +32 -0
- nabu/__init__.py +1 -1
- nabu/pipeline/dataset_validator.py +2 -1
- nabu/pipeline/fullfield/processconfig.py +17 -8
- nabu/pipeline/tests/test_chunk_reader.py +0 -4
- nabu/reconstruction/rings_cuda.py +25 -10
- nabu/utils.py +0 -13
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/METADATA +1 -1
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/RECORD +13 -13
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/WHEEL +1 -1
- nabu/app/tests/__init__.py +0 -0
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/LICENSE +0 -0
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/entry_points.txt +0 -0
- {nabu-2024.1.2.dist-info → nabu-2024.1.4.dist-info}/top_level.txt +0 -0
doc/doc_config.py
ADDED
@@ -0,0 +1,32 @@
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#!/usr/bin/env python
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from nabu.resources.nabu_config import nabu_config
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def generate(file_):
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def write(content):
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print(content, file=file_)
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for section, values in nabu_config.items():
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if section == "about":
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continue
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write("## %s\n" % section)
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for key, val in values.items():
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if val["type"] == "unsupported":
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continue
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write(val["help"] + "\n")
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write(
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"```ini\n%s = %s\n```"
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% (key, val["default"])
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)
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if __name__ == "__main__":
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import sys, os
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print(os.path.abspath(__file__))
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exit(0)
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fname = "/tmp/test.md"
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with open(fname, "w") as f:
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generate(f)
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nabu/__init__.py
CHANGED
@@ -157,8 +157,9 @@ class DatasetValidatorBase:
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"""
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dataset_cfg = self.nabu_config["dataset"]
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self.binning = (dataset_cfg["binning"], dataset_cfg["binning_z"])
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-
subsampling_factor,
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subsampling_factor, subsampling_start = dataset_cfg["projections_subsampling"]
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self.subsampling_factor = subsampling_factor or 1
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self.subsampling_start = subsampling_start or 0
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if self.binning != (1, 1):
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bin_x, bin_z = self.binning
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@@ -83,6 +83,10 @@ class ProcessConfig(ProcessConfigBase):
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)
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self.rec_params = self.nabu_config["reconstruction"]
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subsampling_factor, subsampling_start = self.nabu_config["dataset"]["projections_subsampling"]
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self.subsampling_factor = subsampling_factor or 1
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self.subsampling_start = subsampling_start or 0
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self._update_dataset_with_user_overwrites()
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self._get_rotation_axis_position()
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self._update_rotation_angles()
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@@ -118,8 +122,9 @@ class ProcessConfig(ProcessConfigBase):
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if transl_file is not None and "://" not in transl_file:
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try:
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translations = get_values_from_file(
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transl_file, shape=(self.
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transl_file, shape=(self.n_angles(subsampling=False), last_dim), any_size=True
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).astype(np.float32)
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translations = translations[self.subsampling_start :: self.subsampling_factor]
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except ValueError:
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print("Something wrong with translation_movements_file %s" % transl_file)
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raise
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@@ -145,9 +150,10 @@ class ProcessConfig(ProcessConfigBase):
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try:
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axis_correction = get_values_from_file(
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axis_correction_file,
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n_values=self.
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n_values=self.n_angles(subsampling=False),
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any_size=True,
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).astype(np.float32)
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axis_correction = axis_correction[self.subsampling_start :: self.subsampling_factor]
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except ValueError:
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print("Something wrong with axis correction file %s" % axis_correction_file)
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raise
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@@ -225,7 +231,7 @@ class ProcessConfig(ProcessConfigBase):
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self.logger.debug("Doing coupled validation")
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self._dataset_validator = FullFieldDatasetValidator(self.nabu_config, self.dataset_info)
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# Not so ideal to propagate fields like this
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for what in ["rec_params", "rec_region", "binning"
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for what in ["rec_params", "rec_region", "binning"]:
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setattr(self, what, getattr(self._dataset_validator, what))
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#
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@@ -255,7 +261,7 @@ class ProcessConfig(ProcessConfigBase):
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def n_angles(self, subsampling=False):
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rot_angles = self.dataset_info.rotation_angles
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if subsampling:
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rot_angles = rot_angles[::
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rot_angles = rot_angles[self.subsampling_start :: self.subsampling_factor]
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return len(rot_angles)
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def radios_shape(self, binning=False, subsampling=False):
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return sorted(self.dataset_info.projections.keys())[::step]
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def rotation_angles(self, subsampling=False):
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start = 0
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step = 1
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if subsampling:
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-
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start = self.subsampling_start
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step = self.subsampling_factor
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return self.dataset_info.rotation_angles[start::step]
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@property
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def rec_roi(self):
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translations = dataset_info.translations
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if translations is not None:
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tasks.append("radios_movements")
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options["radios_movements"] = {"translation_movements": dataset_info.translations
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options["radios_movements"] = {"translation_movements": dataset_info.translations}
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#
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# Sinogram normalization (before half-tomo)
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#
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rec_options["enable_halftomo"] = self.do_halftomo
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rec_options["axis_correction"] = dataset_info.axis_correction
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if dataset_info.axis_correction is not None:
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rec_options["axis_correction"] = rec_options["axis_correction"]
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rec_options["axis_correction"] = rec_options["axis_correction"]
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rec_options["angles"] = np.array(self.rotation_angles(subsampling=True))
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rec_options["angles"] += np.deg2rad(nabu_config["reconstruction"]["angle_offset"])
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voxel_size = dataset_info.pixel_size * 1e-4
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first_sino_odd = reader.data[:, 0, :].copy()
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compacted_dataslices_odd = get_compacted_dataslices_as_sorted_tuples(reader)
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# from spire.utils import ims
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# ims([first_sino_all[::2], first_sino_even, first_sino_all[::2]*1. - first_sino_even])
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# ims([first_sino_all[::2], first_sino_even, first_sino_all[1::2]*1. - first_sino_odd])
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# Check that the compacted data slices are correct
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assert len(compacted_dataslices_all) == len(compacted_dataslices_even) == len(compacted_dataslices_odd)
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for data_slice_all, data_slice_even, data_slice_odd in zip(
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@@ -174,10 +174,15 @@ class CudaMunchDeringer(MunchDeringer):
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self._fft_plans[level].ifft(d_coeffs_f, output=d_coeffs)
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def _destripe_2D(self, d_sino, output):
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if not (d_sino.flags.c_contiguous):
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sino = self.cuda_processing.allocate_array("_d_sino", d_sino.shape, np.float32)
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sino[:] = d_sino[:]
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else:
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sino = d_sino
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if self.padding is not None:
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sino = self.padder.pad(sino)
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# set the "image" for DWT (memcpy D2D)
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self._d_sino.set(
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self._d_sino.set(sino)
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# perform forward DWT
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self.cudwt.forward()
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for i in range(self.cudwt.levels):
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filename=get_cuda_srcfile("normalization.cu"),
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signature="PPiii",
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)
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self._mean_kernel_block = (32, 1,
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self._mean_kernel_grid = [updiv(
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self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(
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self._mean_kernel_block = (32, 1, 1)
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self._mean_kernel_grid = [updiv(self.sinos_shape[-1], self._mean_kernel_block[0]), 1, 1]
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self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
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self._mean_kernel_kwargs = {
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"grid": self._mean_kernel_grid,
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"block": self._mean_kernel_block,
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signature="PPiii",
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options=["-DGENERIC_OP=%d" % (3 if self.mode == "divide" else 1)],
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)
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self._op_kernel_block = (16, 16,
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self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[::-1], self._op_kernel_block)]
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self._op_kernel_block = (16, 16, 1)
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self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[1:][::-1], self._op_kernel_block[:-1])] + [
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]
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self._op_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
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self._op_kernel_kwargs = {
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"grid": self._op_kernel_grid,
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"block": self._op_kernel_block,
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if output is not None:
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raise NotImplementedError
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#
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if not (sino.flags.c_contiguous):
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d_sino = self.processing.allocate_array("d_sino", sino.shape, np.float32)
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d_sino[:] = sino[:]
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else:
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d_sino = sino
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self._mean_kernel(d_sino, *self._mean_kernel_args, **self._mean_kernel_kwargs)
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self._apply_filter(self.d_sino_profile)
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self._op_kernel(
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self._op_kernel(d_sino, *self._op_kernel_args, **self._op_kernel_kwargs)
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if not (sino.flags.c_contiguous):
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sino[:] = self.processing.d_sino[:]
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return sino
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def remove_rings_sinograms(self, sinograms):
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nabu/utils.py
CHANGED
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return res
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def remove_first_dict_items(dict_, n_items, sort_func=None, inplace=True):
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"""
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Remove the first items of a dictionary. The keys have to be sortable
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"""
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sorted_keys = sorted(dict_.keys(), key=sort_func)
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if inplace:
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for key in sorted_keys[:n_items]:
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dict_.pop(key)
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return dict_
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else:
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return copy_dict_items(dict_, sorted_keys[n_items:])
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def recursive_copy_dict(dict_):
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"""
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Perform a shallow copy of a dictionary of dictionaries.
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: nabu
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Version: 2024.1.
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Version: 2024.1.4
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Summary: Nabu - Tomography software
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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>
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Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>
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@@ -1,10 +1,11 @@
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doc/conf.py,sha256=3xtCarCHrXPr50GbeRDuH-o3Jzojw7mpr7vpGfZPLAE,3787
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doc/create_conf_doc.py,sha256=IVOdP70KvbW9WS_UQu3Iyd0YfS60E2fJ5IDtQ_s4cDw,1143
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doc/doc_config.py,sha256=anqeOVjqE2e7eVzg7yuh9dvIneTkrA5doGl1cVBqT7Q,730
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doc/get_mathjax.py,sha256=VIvKRCdDuF2VoY8JD3mSey9XX13AZMmwTJBHdt1tUs4,1012
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nabu/__init__.py,sha256=
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nabu/__init__.py,sha256=psl9fotN7bpPsnWf-aTbsiVzq6-RP7bhHXJU3ZsDkwI,270
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nabu/tests.py,sha256=cew9OY2uTyncHI_HM32W8CP6B1GTGKaOW65XtMEqs7o,1417
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nabu/testutils.py,sha256=qqtGgkIhpOpXhgeoXlqCb91Rx-JlI4ALaDF6nt8YRRk,13298
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nabu/utils.py,sha256=
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nabu/utils.py,sha256=w-xfRb6TFQpS-tao6nlvfmr962pmeec-WH1GltSUCrk,23767
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nabu/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/app/bootstrap.py,sha256=UQZzCBKtSXtQp5U0aXtlUhbjbwzgILTI4zD4zVffhBI,3246
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nabu/app/bootstrap_stitching.py,sha256=Inr0_zRAtyeMTK1BKxGqoDf-Na0O33CICmQJYja06ug,2148
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nabu/app/stitching.py,sha256=Ibp1oVokLVMz-VX762j1C0E88Di0YJvRt-b8NjGoe7g,3310
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nabu/app/utils.py,sha256=XUBRWDmth4i3BZHd27rfarFAUP7OEcsMeVmDJ6T4EXA,1178
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nabu/app/validator.py,sha256=IR-DcUV5h1Fc5CChBfBIaglrGpfKNICX7tGirAroMiw,3368
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nabu/app/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/app/tests/test_reduce_dark_flat.py,sha256=T-_zyzD0-f2c5Z-tlzmRF5p3vPtyL2RFb-D5fIYYEoM,2641
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nabu/cuda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/cuda/convolution.py,sha256=n8KsJ7IZdPOs_K5QZC6qblnOvIKYwxtdt03oNa0GiMU,241
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@@ -127,7 +127,7 @@ nabu/pipeline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/pipeline/config.py,sha256=amc05PX0kZA5wHjD1oFP59MfW4pBA-gjBypy4tKLnv0,9221
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nabu/pipeline/config_validators.py,sha256=rvK1Q_KmA1LUeNTefNxXCpYfDQ1zAdk1kFePrLintwc,16300
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nabu/pipeline/datadump.py,sha256=Ua4tbzxfGMOiT2-7WZn3IDiJqzzK-TyFuku_XUkH8_Q,6520
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nabu/pipeline/dataset_validator.py,sha256=
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nabu/pipeline/dataset_validator.py,sha256=etQw9NC_YGsdWCgjsn8aJ3WfvcRuJlLVZlWoqhvvo-8,9263
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nabu/pipeline/detector_distortion_provider.py,sha256=ru1AxbcuO-FA8FYooPBWgp1lzdSDUtzFUC1A_sS8jME,920
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nabu/pipeline/estimators.py,sha256=4V5pwl5vUFMJDanWnmw7POnSsa9lKyKtUzvq9GLcJwc,41374
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nabu/pipeline/fallback_utils.py,sha256=7ccrKYE-rp3fydb72VA6W0_eKcEoqYBEAPlmij_lyEc,6086
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@@ -141,7 +141,7 @@ nabu/pipeline/fullfield/chunked_cuda.py,sha256=aGzjY8MX6OL8auEj6Y0RfOGCmFnczsdfj
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nabu/pipeline/fullfield/computations.py,sha256=VpIURVXh8EpNSfait_AIFM4Ci-GK_546Wkb-Wn9r31Y,9935
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nabu/pipeline/fullfield/dataset_validator.py,sha256=sRgUECUc8aOjFbwrW-dHjvIf7K3T40YPSIgt3cInKAc,3055
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nabu/pipeline/fullfield/nabu_config.py,sha256=a0mMoLkvlvHgX6RmUS1m1UhJS-XB3O6wBCnkNoI90Cs,30358
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nabu/pipeline/fullfield/processconfig.py,sha256=
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nabu/pipeline/fullfield/processconfig.py,sha256=ad2lmo-cCkzfDJqMd__FhbfIInndTxQsLdgH9Ec9Tzc,36107
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nabu/pipeline/fullfield/reconstruction.py,sha256=Km_ZDtoiDQdX3TdTh6E9bzS5hoMC0jYU5eZWodaLbIg,36627
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nabu/pipeline/helical/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/pipeline/helical/dataset_validator.py,sha256=0YQc0hdYdpaXznFaKmlj9SIu7mNs0xXMejcRkhOZHaI,640
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@@ -161,7 +161,7 @@ nabu/pipeline/helical/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
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nabu/pipeline/helical/tests/test_accumulator.py,sha256=nNHwqUgSyUpdZVYNVyxqekj0SoThCF8s-8o3NfSw6vI,6416
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nabu/pipeline/helical/tests/test_pipeline_elements_full.py,sha256=zeR9SaeD0mnhtKU7qo4Qrn_lg1I1Vhg4dqzj6jy8tpg,14569
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nabu/pipeline/helical/tests/test_strategy.py,sha256=rt8SsUHBMMcVFl48kRGcOyf1y4bYqaA2xDznQxE7wFs,2721
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nabu/pipeline/tests/test_chunk_reader.py,sha256=
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nabu/pipeline/tests/test_chunk_reader.py,sha256=OB279hSvgmVhWv_OauZNWTJeaaiheETayGYK79Op10Q,3410
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nabu/pipeline/tests/test_estimators.py,sha256=6VK7fxxfrRTWSSi2bhHqbLy8pZJ2DALO1gJkuxpLDSQ,8392
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nabu/pipeline/xrdct/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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nabu/preproc/__init__.py,sha256=dKxvZvWZXjKS3iPRaSXiUeM2dNGIOyTlirq5pdAWY0Y,284
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@@ -234,7 +234,7 @@ nabu/reconstruction/projection.py,sha256=7WVPlYLUmCmB2yR1JYmVLJ5fZ3CMMKQ3vS9yuTU
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nabu/reconstruction/reconstructor.py,sha256=wSva2EK-NTJi8N_ubzJWIZ4sv2ksfrA9YcA2ioEtISo,7299
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nabu/reconstruction/reconstructor_cuda.py,sha256=m_3GzG44PRyiSEfTvYjgr5atLwl26hMfZOMyqTWxp0g,1644
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nabu/reconstruction/rings.py,sha256=mpbCLuFM_6Uy9oNJkyQ8tZwhGhrbWtzRlArSRsC90bI,9527
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nabu/reconstruction/rings_cuda.py,sha256=
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nabu/reconstruction/rings_cuda.py,sha256=NFU4lV_K6oY3eVyHmK_zxpQYeXpejOe_j8fnK7Vnnb0,13514
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nabu/reconstruction/sinogram.py,sha256=KTSGP_JJABf4Yr9l628HPbyWsBnpbnyGKyPEq3ZrPIE,17026
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nabu/reconstruction/sinogram_cuda.py,sha256=wS84AIy3T00d1kTtuJOQmA3hktbDVs4ybwB9haiBcoY,10623
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nabu/reconstruction/sinogram_opencl.py,sha256=p793N26VknU8KIZLtDgFY6HNx0TylemZ1YL4WKD3fHs,1403
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@@ -288,9 +288,9 @@ nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtC
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nabu/thirdparty/tomocupy_remove_stripe.py,sha256=VgXHr2tzTAAGZix5pwhFfbPxj4tt3yXBcjCPNQSLPAg,22810
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nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
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nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
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nabu-2024.1.
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nabu-2024.1.4.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
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nabu-2024.1.4.dist-info/METADATA,sha256=gJfS07iPzNeEw40J0wzEK8Y7inuscqmakqyZfu7-hFM,5224
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nabu-2024.1.4.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
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nabu-2024.1.4.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
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nabu-2024.1.4.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
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nabu-2024.1.4.dist-info/RECORD,,
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nabu/app/tests/__init__.py
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