nabu 2023.2.1__py3-none-any.whl → 2024.1.0rc3__py3-none-any.whl

{nabu-2023.2.1.dist-info → nabu-2024.1.0rc3.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2023.2.1
+Version: 2024.1.0rc3
 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>
 License: MIT License
         
-        Copyright (c) 2020-2023 ESRF
+        Copyright (c) 2020-2024 ESRF
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -53,7 +53,7 @@ Requires-Dist: numpy >1.9.0
 Requires-Dist: scipy
 Requires-Dist: h5py >=3.0
 Requires-Dist: silx >=0.15.0
-Requires-Dist: tomoscan <2.0,>=1.3.2
+Requires-Dist: tomoscan >=2.0.0a7
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile
@@ -69,8 +69,8 @@ Requires-Dist: glymur ; extra == 'full'
 Requires-Dist: pycuda ; extra == 'full'
 Requires-Dist: scikit-cuda ; extra == 'full'
 Requires-Dist: pycudwt ; extra == 'full'
-Requires-Dist: sluurp >=0.2 ; extra == 'full'
-Requires-Dist: nxtomomill <1.0,>=0.12.3 ; extra == 'full'
+Requires-Dist: sluurp >=0.3 ; extra == 'full'
+Requires-Dist: pyvkfft ; extra == 'full'
 
 # Nabu
 

nabu-2024.1.0rc3.dist-info/RECORD

@@ -0,0 +1,296 @@
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+nabu/thirdparty/algotom_convert_sino.py,sha256=iZVRilvyqMyLTu8RKgbqDFUjObWW5X69rCARrnNizuI,13872
+nabu/thirdparty/pore3d_deringer_munch.py,sha256=o4bisnFc-wMjuohWBT8wgWmfNehPQGtCl6G2NebJlbg,4500
+nabu/thirdparty/tomocupy_remove_stripe.py,sha256=VgXHr2tzTAAGZix5pwhFfbPxj4tt3yXBcjCPNQSLPAg,22810
+nabu/thirdparty/tomopy_phase.py,sha256=hK4oPpkogLOhv23XzzEXQY2u3r8fJvASY_bINVs6ERE,8634
+nabu/thirdparty/tomwer_load_flats_darks.py,sha256=ZNoVAinUb_wGYbfvs_4BVnWsjsQmNxSvCh1bWhR2WWg,5611
+nabu-2024.1.0rc3.dist-info/LICENSE,sha256=1eAIPSnEsnSFNUODnLtNtQTs76exG3ZxJ1DJR6zoUBA,1066
+nabu-2024.1.0rc3.dist-info/METADATA,sha256=q6_cXr8-lpZGerhGxTc_pnfMqRob6c0KXEbSL8Xv4d4,5229
+nabu-2024.1.0rc3.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+nabu-2024.1.0rc3.dist-info/entry_points.txt,sha256=cJKGkBeykVL7uK3E4R0RLRqMXifTL2qdO573syPAvJc,1288
+nabu-2024.1.0rc3.dist-info/top_level.txt,sha256=fsm_N3eXLRZk2QXF9OSKPNDPFXOz8FAQjHh5avT3dok,9
+nabu-2024.1.0rc3.dist-info/RECORD,,

{nabu-2023.2.1.dist-info → nabu-2024.1.0rc3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.1)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{nabu-2023.2.1.dist-info → nabu-2024.1.0rc3.dist-info}/entry_points.txt

@@ -4,13 +4,17 @@ nabu-cast = nabu.app.cast_volume:main
 nabu-compare-volumes = nabu.app.compare_volumes:compare_volumes_cli
 nabu-composite-cor = nabu.app.composite_cor:main
 nabu-config = nabu.app.bootstrap:bootstrap
+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-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-poly2map = nabu.app.create_distortion_map_from_poly:horizontal_match_entry_point
+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-shrink-dataset = nabu.app.shrink_dataset:shrink_cli

nabu/conftest.py

@@ -1,14 +0,0 @@
-import pytest
-from tomoscan.test.utils import HDF5MockContext
-
-
-@pytest.fixture(scope="function")
-def hdf5_scan(tmp_path):
-    """simple fixture to create a scan and provide it to another function"""
-    test_dir = tmp_path / "my_hdf5_scan"
-    with HDF5MockContext(
-        scan_path=str(test_dir),
-        n_proj=10,
-        n_ini_proj=10,
-    ) as scan:
-        yield scan

nabu/opencl/fftshift.py

@@ -1,92 +0,0 @@
-import numpy as np
-from ..utils import get_opencl_srcfile, updiv, check_supported
-from .kernel import OpenCLKernel
-from .processing import OpenCLProcessing
-import pyopencl.array as parray
-from pyopencl.tools import dtype_to_ctype
-
-'''
-class OpenCLfftshift:
-    def __init__(
-        self,
-        shape,
-        dtype,
-        axes=None,
-        opencl_options=None,
-    ):
-        self.opencl_processing = OpenCLProcessing(**(opencl_options or {}))
-        self._set_shape_axes(shape, axes)
-        self._set_dtype(dtype)
-
-    def _set_shape_axes(self, shape, axes):
-        ...  # TODO
-
-    def _set_dtype(self, dtype):
-        self.dtype = dtype
-        self.dtype_c = dtype_to_ctype(self.dtype)
-
-    def _init_kernel(self):
-        self.fftshift = OpenCLKernel(
-            kernel_name,
-            self.opencl_processing.ctx,
-            filename=get_opencl_srcfile("fftshift.cl"),
-            options=["-DDTYPE=%s" % self.dtype_c],
-        )
-
-    def _init_opencl_coordinate_transform(self):
-        if self.mode == "constant":
-            self.d_padded_array_constant = parray.to_device(self.queue, self.padded_array_constant)
-            self.memcpy2D = OpenCLMemcpy2D(ctx=self.opencl_processing.ctx, queue=self.queue)
-            return
-        self._coords_transform_kernel = OpenCLKernel(
-            "coordinate_transform",
-            self.opencl_processing.ctx,
-            filename=get_opencl_srcfile("padding.cl"),
-        )
-        self._coords_transform_local_size = (16, 16, 1)
-        self._coords_transform_global_size = [
-            updiv(a, b) for a, b in zip(self.padded_shape[::-1], self._coords_transform_local_size)
-        ]
-        self.d_coords_rows = parray.to_device(self.queue, self.coords_rows)
-        self.d_coords_cols = parray.to_device(self.queue, self.coords_cols)
-
-    def _pad_constant(self, image, output):
-        pad_y, pad_x = self.pad_width
-        # the following line is not implemented in pyopencl
-        # self.d_padded_array_constant[pad_y[0] : pad_y[0] + self.shape[0], pad_x[0] : pad_x[0] + self.shape[1]] = image[:]
-        # cl.enqueue_copy is too cumbersome to use for Buffer <-> Buffer.
-        # Use a dedicated kernel instead.
-        # This is not optimal (two copies) - TODO write a constant padding kernel
-        self.memcpy2D(self.d_padded_array_constant, image, image.shape[::-1], dst_offset_xy=(pad_x[0], pad_y[0]))
-        output[:] = self.d_padded_array_constant[:]
-        return output
-
-    def pad(self, image, output=None):
-        """
-        Pad an array.
-
-        Parameters
-        ----------
-        image: pycuda.gpuarray.GPUArray
-            Image to pad
-        output: pycuda.gpuarray.GPUArray, optional
-            Output image. If provided, must be in the expected shape.
-        """
-        if output is None:
-            output = self.opencl_processing.allocate_array("d_output", self.padded_shape)
-        if self.mode == "constant":
-            return self._pad_constant(image, output)
-        self._coords_transform_kernel(
-            self.queue,
-            image,
-            output,
-            self.d_coords_cols,
-            self.d_coords_rows,
-            np.int32(self.shape[1]),
-            np.int32(self.padded_shape[1]),
-            np.int32(self.padded_shape[0]),
-            global_size=self._coords_transform_global_size,
-            local_size=self._coords_transform_local_size,
-        )
-        return output
-'''

nabu/opencl/tests/test_fftshift.py

@@ -1,55 +0,0 @@
-"""
-import numpy as np
-import pytest
-from nabu.opencl.utils import __has_pyopencl__, get_opencl_context
-from nabu.utils import calc_padding_lengths, get_opencl_srcfile
-from nabu.testutils import get_data, generate_tests_scenarios, __do_long_tests__
-
-if __has_pyopencl__:
-    import pyopencl.array as parray
-    from nabu.opencl.fftshift import OpenCLfftshift
-
-
-scenarios = generate_tests_scenarios(
-    {
-        "shape": [(511, 512), (512, 511)],
-        "pad_width": [((256, 255), (128, 127)), ((0, 0), (6, 7))],
-        "mode": OpenCLPadding.supported_modes if __has_pyopencl__ else [],
-        "constant_values": [0, ((1.0, 2.0), (3.0, 4.0))],
-        "output_is_none": [True, False],
-    }
-)
-
-
-@pytest.fixture(scope="class")
-def bootstrap(request):
-    cls = request.cls
-    cls.data = get_data('brain_phantom.npz')['data']
-    cls.tol = 1e-7
-    cls.ctx = get_opencl_context("all")
-    yield
-
-
-@pytest.mark.skipif(not (__has_pyopencl__), reason="Need OpenCL and pyopencl for this test")
-@pytest.mark.usefixtures("bootstrap")
-class TestOpenCLFFTshift:
-    @pytest.mark.parametrize("config", scenarios)
-    def test_fftshift(self, config):
-        direction = config["direction"]
-        shape = config["shape"]
-        dtype = config["dtype"]
-
-        data = np.squeeze(self.data[: shape[0], : shape[1]]).astype(dtype)  # can be 1D or 2D
-
-        shifter = OpenCLfftshift(data.shape, data.dtype, opencl_options={"ctx": self.ctx})
-        queue = shifter.queue
-        d_data = parray.to_device(queue, data)
-        shifter(d_data)  # in-place
-        res = d_data.get()
-
-        reference_shifter = np.fft.fftshift if direction == "forward" else np.fft.ifftshift
-        ref = reference_shifter(x, axes=config["axes"])
-
-        err_max = np.max(np.abs(res - ref))
-        assert err_max < self.tol, str("Something wrong with fftshift for configuration %s" % (str(config)))
-"""

nabu/opencl/tests/test_padding.py

@@ -1,84 +0,0 @@
-import numpy as np
-import pytest
-from nabu.opencl.utils import __has_pyopencl__, get_opencl_context
-from nabu.utils import calc_padding_lengths, get_opencl_srcfile
-from nabu.testutils import get_data, generate_tests_scenarios
-
-if __has_pyopencl__:
-    import pyopencl.array as parray
-    from nabu.opencl.kernel import OpenCLKernel
-    from nabu.opencl.padding import OpenCLPadding
-
-
-scenarios = generate_tests_scenarios(
-    {
-        "shape": [(511, 512), (512, 511)],
-        "pad_width": [((256, 255), (128, 127)), ((0, 0), (6, 7))],
-        "mode": OpenCLPadding.supported_modes if __has_pyopencl__ else [],
-        "constant_values": [0, ((1.0, 2.0), (3.0, 4.0))],
-        "output_is_none": [True, False],
-    }
-)
-
-
-@pytest.fixture(scope="class")
-def bootstrap(request):
-    cls = request.cls
-    cls.data = get_data("brain_phantom.npz")["data"]
-    cls.tol = 1e-7
-    cls.ctx = get_opencl_context("all")
-    yield
-
-
-@pytest.mark.skipif(not (__has_pyopencl__), reason="Need OpenCL and pyopencl for this test")
-@pytest.mark.usefixtures("bootstrap")
-class TestOpenCLPadding:
-    @pytest.mark.parametrize("config", scenarios)
-    def test_padding(self, config):
-        shape = config["shape"]
-        data = self.data[: shape[0], : shape[1]]
-        kwargs = {}
-        if config["mode"] == "constant":
-            kwargs["constant_values"] = config["constant_values"]
-        ref = np.pad(data, config["pad_width"], mode=config["mode"], **kwargs)
-        opencl_padding = OpenCLPadding(
-            config["shape"],
-            config["pad_width"],
-            mode=config["mode"],
-            constant_values=config["constant_values"],
-            opencl_options={"ctx": self.ctx},
-        )
-        queue = opencl_padding.queue
-        d_img = parray.to_device(queue, np.ascontiguousarray(data, dtype="f"))
-        if config["output_is_none"]:
-            output = None
-        else:
-            output = parray.zeros(queue, ref.shape, "f")
-        res = opencl_padding.pad(d_img, output=output)
-
-        err_max = np.max(np.abs(res.get() - ref))
-        assert err_max < self.tol, str("Something wrong with padding for configuration %s" % (str(config)))
-
-    def test_custom_coordinate_transform(self):
-        data = self.data
-        R, C = np.indices(data.shape, dtype=np.int32)
-
-        pad_width = ((256, 255), (254, 251))
-        mode = "reflect"
-
-        coords_R = np.pad(R, pad_width, mode=mode)
-        coords_C = np.pad(C, pad_width, mode=mode)
-        # Further transform of coordinates - here FFT layout
-        coords_R = np.roll(coords_R, (-pad_width[0][0], -pad_width[1][0]), axis=(0, 1))
-        coords_C = np.roll(coords_C, (-pad_width[0][0], -pad_width[1][0]), axis=(0, 1))
-
-        opencl_padding = OpenCLPadding(data.shape, (coords_R, coords_C), mode=mode, opencl_options={"ctx": self.ctx})
-        queue = opencl_padding.queue
-        d_img = parray.to_device(queue, data)
-        d_out = parray.zeros(queue, opencl_padding.padded_shape, "f")
-        res = opencl_padding.pad(d_img, output=d_out)
-
-        ref = np.roll(np.pad(data, pad_width, mode=mode), (-pad_width[0][0], -pad_width[1][0]), axis=(0, 1))
-
-        err_max = np.max(np.abs(d_out.get() - ref))
-        assert err_max < self.tol, "Something wrong with custom padding"