nabu 2024.1.0rc3__py3-none-any.whl → 2024.1.1__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_flatfield.py

@@ -0,0 +1,626 @@
+from tempfile import mkdtemp
+import os
+import numpy as np
+import pytest
+from silx.io.url import DataUrl
+from silx.io import get_data
+from silx.io.dictdump import dicttoh5
+from nabu.cuda.utils import get_cuda_context, __has_pycuda__
+from nabu.preproc.flatfield import FlatField, FlatFieldDataUrls
+
+if __has_pycuda__:
+    import pycuda.gpuarray as garray
+    from nabu.preproc.flatfield_cuda import CudaFlatFieldDataUrls, CudaFlatField
+
+
+# Flats values should be O(k) so that linear interpolation between flats gives exact results
+flatfield_tests_cases = {
+    "simple_nearest_interp": {
+        "image_shape": (100, 512),
+        "radios_values": np.arange(10) + 1,
+        "radios_indices": None,
+        "flats_values": [0.5],
+        "flats_indices": [1],
+        "darks_values": [1],
+        "darks_indices": [0],
+        "expected_result": np.arange(0, -2 * 10, -2),
+    },
+    "two_flats_no_radios_indices": {
+        "image_shape": (100, 512),
+        "radios_values": np.arange(10) + 1,
+        "radios_indices": None,
+        "flats_values": [2, 11],
+        "flats_indices": [0, 9],
+        "darks_values": [1],
+        "darks_indices": [0],
+        "expected_result": np.arange(10) / (np.arange(10) + 1),
+    },
+    "two_flats_with_radios_indices": {
+        #  Type     D   F   R   R   R   F
+        #  IDX      0   1   2   3   4   5
+        #  Value    1   4   9   16  25  8
+        #  F_interp         5   6   7
+        "image_shape": (16, 17),
+        # R_k = (k + 1)**2
+        "radios_values": [9, 16, 25],
+        "radios_indices": [2, 3, 4],
+        # F_k = k+3
+        "flats_values": [4, 8],
+        "flats_indices": [1, 5],
+        # D_k = 1
+        "darks_values": [1],
+        "darks_indices": [0],
+        # Expected normalization result: N_k = k
+        "expected_result": [2, 3, 4],
+    },
+    "three_flats_srcurrent": {
+        #  Type     D   F   R   R  | R   F   R   R   F
+        #  IDX      0   1   2   3  | 4   5   6   7   8
+        #  Value    1   4   9   16 | 25  8   46  67  14
+        #  F_interp         5   6  | 7       10  12
+        #  srCurrent    20  10  10 | 16  32  16  8  16
+        "image_shape": (16, 17),
+        "radios_values": [9, 16, 25, 46, 67],
+        "radios_indices": [2, 3, 4, 6, 7],
+        "flats_values": [4, 8, 14],
+        "flats_indices": [1, 5, 8],
+        "darks_values": [1],
+        "darks_indices": [0],
+        # "expected_result": [2, 3, 4, 5, 6], # without SR normalization
+        "expected_result": [4, 6, 8, 10, 12],
+        # sr_flat/sr_radio = 2
+        "radios_srcurrent": [10, 16, 16, 16, 8],
+        # "flats_srcurrent": [20, 18, 6, 4, 2],
+        "flats_srcurrent": [20, 32, 16],
+    },
+}
+
+
+def generate_test_flatfield_generalized(
+    image_shape,
+    radios_indices,
+    radios_values,
+    flats_indices,
+    flats_values,
+    darks_indices,
+    darks_values,
+    h5_fname,
+    dtype=np.uint16,
+):
+    """
+    Parameters
+    -----------
+    image_shape: tuple of int
+        shape of each image.
+    radios_indices: array of int
+        Indices where radios are found in the dataset.
+    radios_values: array of scalars
+        Value for each radio image.
+        Length must be equal to `radios_shape[0]`.
+    flats_indices: array of int
+        Indices where flats are found in the dataset.
+    flats_values: array of scalars
+        Values of flat images.
+        Length must be equal to `len(flats_indices)`
+    darks_indices: array of int
+        Indices where darks are found in the dataset.
+    darks_values: array of scalars
+        Values of dark images.
+        Length must be equal to `len(darks_indices)`
+
+    Returns
+    -------
+    radios: numpy.ndarray
+        3D array with raw radios
+    darks: dict of DataUrls
+        Dictionary where each key is the dark indice, and value is a DataUrl
+    flats: dict of DataUrls
+        Dictionary where each key is the flat indice, and value is a DataUrl
+    """
+    tempdir = mkdtemp(prefix="nabu_")
+    testffname = os.path.join(tempdir, h5_fname)
+
+    # Radios
+    radios = np.zeros((len(radios_values),) + image_shape, dtype="f")
+    n_radios = radios.shape[0]
+    for i in range(n_radios):
+        radios[i].fill(radios_values[i])
+    img_shape = radios.shape[1:]
+
+    # Flats
+    flats = {}
+    flats_urls = {}
+    for i, flat_idx in enumerate(flats_indices):
+        flats["flats_%06d" % flat_idx] = np.zeros(img_shape, dtype=dtype) + flats_values[i]
+        flats_urls[flat_idx] = DataUrl(
+            file_path=testffname, data_path=str("/flats/flats_%06d" % flat_idx), scheme="silx"
+        )
+
+    # Darks
+    darks = {}
+    darks_urls = {}
+    for i, dark_idx in enumerate(darks_indices):
+        darks["darks_%06d" % dark_idx] = np.zeros(img_shape, dtype=dtype) + darks_values[i]
+        darks_urls[dark_idx] = DataUrl(
+            file_path=testffname, data_path=str("/darks/darks_%06d" % dark_idx), scheme="silx"
+        )
+
+    dicttoh5(flats, testffname, h5path="/flats", mode="w")
+    dicttoh5(darks, testffname, h5path="/darks", mode="a")
+
+    return radios, flats_urls, darks_urls
+
+
+@pytest.fixture(scope="class")
+def bootstrap(request):
+    cls = request.cls
+    cls.tmp_files = []
+    cls.tmp_dirs = []
+    cls.n_radios = 10
+    cls.n_z = 100
+    cls.n_x = 512
+    if __has_pycuda__:
+        cls.ctx = get_cuda_context()
+    yield
+    # Tear-down
+    for fname in cls.tmp_files:
+        os.remove(fname)
+    for dname in cls.tmp_dirs:
+        os.rmdir(dname)
+
+
+@pytest.mark.usefixtures("bootstrap")
+class TestFlatField:
+    def get_test_elements(self, case_name):
+        config = flatfield_tests_cases[case_name]
+        radios_stack, flats_url, darks_url = generate_test_flatfield_generalized(
+            config["image_shape"],
+            config["radios_indices"],
+            config["radios_values"],
+            config["flats_indices"],
+            config["flats_values"],
+            config["darks_indices"],
+            config["darks_values"],
+            "test_ff.h5",
+        )
+        fname = flats_url[list(flats_url.keys())[0]].file_path()
+        self.tmp_files.append(fname)
+        self.tmp_dirs.append(os.path.dirname(fname))
+        return radios_stack, flats_url, darks_url, config
+
+    @staticmethod
+    def check_normalized_radios(radios_corr, expected_values):
+        # must be the same value everywhere in the radio
+        std = np.std(np.std(radios_corr, axis=-1), axis=-1)
+        assert np.max(np.abs(std)) < 1e-7
+        # radios values must be 0, -2, -4, ...
+        assert np.allclose(radios_corr[:, 0, 0], expected_values)
+
+    def test_flatfield_simple(self):
+        """
+        Test the flat-field normalization on a radios stack with 1 dark and 1 flat.
+
+        (I - D)/(F - D)   where I = (1, 2, ...), D = 1, F = 0.5
+        = (0, -2, -4, -6, ...)
+        """
+        radios_stack, flats_url, darks_url, config = self.get_test_elements("simple_nearest_interp")
+
+        flatfield = FlatFieldDataUrls(radios_stack.shape, flats_url, darks_url)
+        radios_corr = flatfield.normalize_radios(np.copy(radios_stack))
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+    def test_flatfield_simple_subregion(self):
+        """
+        Same as test_flatfield_simple, but in a vertical subregion of the radios.
+        """
+        radios_stack, flats_url, darks_url, config = self.get_test_elements("simple_nearest_interp")
+        end_z = 51
+        radios_chunk = np.copy(radios_stack[:, :end_z, :])
+        # we only have a chunk in memory. Instantiate the class with the
+        # corresponding subregion to only load the relevant part of dark/flat
+        flatfield = FlatFieldDataUrls(
+            radios_chunk.shape,
+            flats_url,
+            darks_url,
+            sub_region=(None, None, None, end_z),  # start_x, end_x, start_z, end_z
+        )
+        radios_corr = flatfield.normalize_radios(radios_chunk)
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+    def test_flatfield_linear_interp(self):
+        """
+        Test flat-field normalization with 1 dark and 2 flats, with linear
+        interpolation between flats.
+        I   = 1   2   3   4   5   6   7   8   9   10
+        D   = 1                                         (one dark)
+        F   = 2                                   11    (two flats)
+        F_i = 2   3   4   5   6   7   8   9   10  11   (interpolated flats)
+        R   = 0  .5  .66 .75 .8  .83  .86
+            = (I-D)/(F-D)
+            = (I-1)/I
+        """
+        radios_stack, flats_url, darks_url, config = self.get_test_elements("two_flats_no_radios_indices")
+        flatfield = FlatFieldDataUrls(radios_stack.shape, flats_url, darks_url)
+        radios_corr = flatfield.normalize_radios(np.copy(radios_stack))
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+        # Test 2: one of the flats is not at the beginning/end
+        # I   = 1    2    3    4    5    6    7    8    9    10
+        # F   = 2                       11
+        # F_i = 2   3.8  5.6 7.4  9.2   11   11   11   11    11
+        # R   = 0   .357  .435 .469 .488 .5  .6   .7  .8     .9
+        flats_url = flats_url.copy()
+        flats_url[5] = flats_url[9]
+        flats_url.pop(9)
+        flatfield = FlatFieldDataUrls(radios_stack.shape, flats_url, darks_url)
+        radios_corr = flatfield.normalize_radios(np.copy(radios_stack))
+        self.check_normalized_radios(
+            radios_corr, [0.0, 0.35714286, 0.43478261, 0.46875, 0.48780488, 0.5, 0.6, 0.7, 0.8, 0.9]
+        )
+
+    @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
+    def test_cuda_flatfield(self):
+        """
+        Test the flat-field with cuda back-end.
+        """
+        radios_stack, flats_url, darks_url, config = self.get_test_elements("two_flats_no_radios_indices")
+        d_radios = garray.to_gpu(radios_stack.astype("f"))
+        cuda_flatfield = CudaFlatFieldDataUrls(
+            d_radios.shape,
+            flats_url,
+            darks_url,
+        )
+        cuda_flatfield.normalize_radios(d_radios)
+        radios_corr = d_radios.get()
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+    # Linear interpolation, two flats, one dark
+    def test_twoflats_simple(self):
+        radios, flats, darks, config = self.get_test_elements("two_flats_with_radios_indices")
+        FF = FlatFieldDataUrls(radios.shape, flats, darks, radios_indices=config["radios_indices"])
+        FF.normalize_radios(radios)
+        self.check_normalized_radios(radios, config["expected_result"])
+
+    def _setup_numerical_issue(self):
+        radios, flats, darks, config = self.get_test_elements("two_flats_with_radios_indices")
+
+        # Retrieve the actual data for radios/darks/flats to use FlatField instead of FlatFieldDataUrl.
+        # Create a setting yielding "0/0": one pixel such that flat==dark and radio==dark
+        for flat_idx, flat_url in flats.items():
+            flats[flat_idx] = get_data(flat_url)
+            flats[flat_idx][0, 0] = 99
+        for dark_idx, dark_url in darks.items():
+            darks[dark_idx] = get_data(dark_url)
+            darks[dark_idx][0, 0] = 99
+        radios[:, 0, 0] = 99
+        return radios, flats, darks, config
+
+    def _check_numerical_issue(self, radios, expected_result, nan_value=None):
+        if nan_value is None:
+            assert np.alltrue(np.logical_not(np.isfinite(radios[:, 0, 0]))), "First pixel should be nan or inf"
+            radios[:, 0, 0] = radios[:, 1, 1]
+            self.check_normalized_radios(radios, expected_result)
+        else:
+            assert np.all(np.isfinite(radios)), "No inf/nan value should be there"
+            assert np.allclose(radios[:, 0, 0], nan_value, atol=1e-7), (
+                "Handled NaN should have nan_value=%f" % nan_value
+            )
+            radios[:, 0, 0] = radios[:, 1, 1]
+            self.check_normalized_radios(radios, expected_result)
+
+    def test_twoflats_numerical_issue(self):
+        """
+        Same as above, but for the first radio: I==Dark and Flat==Dark
+        For this radio, nan is replaced with 1.
+        """
+        radios, flats, darks, config = self._setup_numerical_issue()
+        radios0 = radios.copy()
+
+        # FlatField without NaN handling yields NaN and raises RuntimeWarning
+        FF_no_nan_handling = FlatField(
+            radios.shape, flats, darks, radios_indices=config["radios_indices"], nan_value=None
+        )
+        with pytest.warns(RuntimeWarning):
+            FF_no_nan_handling.normalize_radios(radios)
+        self._check_numerical_issue(radios, config["expected_result"], None)
+
+        # FlatField with NaN handling
+        nan_value = 50
+        radios = radios0.copy()
+        FF_with_nan_handling = FlatField(
+            radios.shape, flats, darks, radios_indices=config["radios_indices"], nan_value=nan_value
+        )
+        with pytest.warns(RuntimeWarning):
+            FF_with_nan_handling.normalize_radios(radios)
+        self._check_numerical_issue(radios, config["expected_result"], nan_value)
+
+    @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
+    def test_cuda_twoflats_numerical_issue(self):
+        """
+        Same as above, with the Cuda backend
+        """
+        radios, flats, darks, config = self._setup_numerical_issue()
+        radios0 = radios.copy()
+        d_radios = garray.to_gpu(radios)
+        FF_no_nan_handling = CudaFlatField(
+            radios.shape, flats, darks, radios_indices=config["radios_indices"], nan_value=None
+        )
+        # In a cuda kernel, no one can hear you scream
+        FF_no_nan_handling.normalize_radios(d_radios)
+        radios = d_radios.get()
+        self._check_numerical_issue(radios, config["expected_result"], None)
+
+        # FlatField with NaN handling
+        nan_value = 50
+        d_radios.set(radios0)
+        FF_with_nan_handling = CudaFlatField(
+            radios.shape, flats, darks, radios_indices=config["radios_indices"], nan_value=nan_value
+        )
+        FF_with_nan_handling.normalize_radios(d_radios)
+        radios = d_radios.get()
+        self._check_numerical_issue(radios, config["expected_result"], nan_value)
+
+    def test_srcurrent(self):
+        radios, flats, darks, config = self.get_test_elements("three_flats_srcurrent")
+
+        FF = FlatFieldDataUrls(
+            radios.shape,
+            flats,
+            darks,
+            radios_indices=config["radios_indices"],
+            radios_srcurrent=config["radios_srcurrent"],
+            flats_srcurrent=config["flats_srcurrent"],
+        )
+        radios_corr = FF.normalize_radios(np.copy(radios))
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+    @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
+    def test_srcurrent_cuda(self):
+        radios, flats, darks, config = self.get_test_elements("three_flats_srcurrent")
+        d_radios = garray.to_gpu(radios)
+
+        FF = CudaFlatFieldDataUrls(
+            radios.shape,
+            flats,
+            darks,
+            radios_indices=config["radios_indices"],
+            radios_srcurrent=config["radios_srcurrent"],
+            flats_srcurrent=config["flats_srcurrent"],
+        )
+        FF.normalize_radios(d_radios)
+        radios_corr = d_radios.get()
+        self.check_normalized_radios(radios_corr, config["expected_result"])
+
+
+# This test should be closer to the ESRF standard setting.
+# There are 2 flats, one dark, 4000 radios.
+#  dark :  indice=0     value=10
+#  flat1 : indice=1     value=4202
+#  flat2 : indice=2102  value=2101
+#
+# The projections have the following indices:
+#  j:    0     1        1998  1999  2000  2001                   3999
+# idx:  [102, 103, ..., 2100, 2101, 2203, 2204, ..., 4200, 4201, 4202]
+#  Notice the gap in the middle.
+#
+# The linear interpolation is
+#    flat_i = (n2 - i)/(n2 - n1)*flat_1  + (i - n1)/(n2 - n1)*flat_2
+#  where n1 and n2 are the indices of flat_1 and flat_2 respectively.
+# With the above values, we have flat_i = 4203 - i.
+#
+# The projections values are dark + i*(flat_i - dark),
+# so that the normalization norm_i = (proj_i - dark)/(flat_i - dark) gives
+#
+#   idx     102    103    104    ...
+#   flat    4101   4102   4103   ...
+#   norm    102    103    104    ...
+#
+
+
+class FlatFieldTestDataset:
+    # Parameters
+    shp = (27, 32)
+    n1 = 1  # flat indice 1
+    n2 = 2102  # flat indice 2
+    dark_val = 10
+    darks = {0: np.zeros(shp, "f") + dark_val}
+    flats = {n1: np.zeros(shp, "f") + (n2 - 1) * 2, n2: np.zeros(shp, "f") + n2 - 1}
+    projs_idx = list(range(102, 2102)) + list(range(2203, 4203))  # gap in the middle
+
+    def __init__(self):
+        self._generate_projections()
+        self._dump_to_h5()
+        self._generate_dataurls()
+
+    def get_flat_idx(self, proj_idx):
+        flats_idx = sorted(list(self.flats.keys()))
+        if proj_idx <= flats_idx[0]:
+            return (flats_idx[0],)
+        elif proj_idx > flats_idx[0] and proj_idx < flats_idx[1]:
+            return flats_idx
+        else:
+            return (flats_idx[1],)
+
+    def get_flat(self, idx):
+        flatidx = self.get_flat_idx(idx)
+        if len(flatidx) == 1:
+            flat = self.flats[flatidx[0]]
+        else:
+            nf1, nf2 = flatidx
+            w1 = (nf2 - idx) / (nf2 - nf1)
+            flat = w1 * self.flats[nf1] + (1 - w1) * self.flats[nf2]
+        return flat
+
+    def _generate_projections(self):
+        self.projs_data = np.zeros((len(self.projs_idx),) + self.shp, "f")
+        self.projs = {}
+        for i, proj_idx in enumerate(self.projs_idx):
+            flat = self.get_flat(proj_idx)
+
+            proj_val = self.dark_val + proj_idx * (flat[0, 0] - self.dark_val)
+            self.projs[str(proj_idx)] = np.zeros(self.shp, "f") + proj_val
+            self.projs_data[i] = self.projs[str(proj_idx)]
+
+    def _dump_to_h5(self):
+        self.tempdir = mkdtemp(prefix="nabu_")
+        self.fname = os.path.join(self.tempdir, "projs_flats.h5")
+        dicttoh5(
+            {
+                "projs": self.projs,
+                "flats": {str(k): v for k, v in self.flats.items()},
+                "darks": {str(k): v for k, v in self.darks.items()},
+            },
+            h5file=self.fname,
+        )
+
+    def _generate_dataurls(self):
+        self.flats_urls = {}
+        for idx in self.flats.keys():
+            self.flats_urls[int(idx)] = DataUrl(file_path=self.fname, data_path="/flats/%d" % idx)
+        self.darks_urls = {}
+        for idx in self.darks.keys():
+            self.darks_urls[int(idx)] = DataUrl(file_path=self.fname, data_path="/darks/0")
+
+
+@pytest.fixture(scope="class")
+def bootstraph5(request):
+    cls = request.cls
+
+    cls.dataset = FlatFieldTestDataset()
+    n1, n2 = cls.dataset.n1, cls.dataset.n2
+
+    # Interpolation function
+    cls._weight1 = lambda i: (n2 - i) / (n2 - n1)
+
+    cls.tol = 5e-4
+    cls.tol_std = 1e-3
+
+    yield
+    # tear-down
+    os.remove(cls.dataset.fname)
+    os.rmdir(cls.dataset.tempdir)
+
+
+@pytest.mark.usefixtures("bootstraph5")
+class TestFlatFieldH5:
+    def check_normalization(self, projs):
+        # Check that each projection is filled with the same values
+        std_projs = np.std(projs, axis=(-2, -1))
+        assert np.max(np.abs(std_projs)) < self.tol_std
+        # Check that the normalized radios are equal to 102, 103, 104, ...
+        errs = projs[:, 0, 0] - self.dataset.projs_idx
+        assert np.max(np.abs(errs)) < self.tol, "Something wrong with flat-field normalization"
+
+    def test_flatfield(self):
+        flatfield = FlatFieldDataUrls(
+            self.dataset.projs_data.shape,
+            self.dataset.flats_urls,
+            self.dataset.darks_urls,
+            radios_indices=self.dataset.projs_idx,
+            interpolation="linear",
+        )
+        projs = np.copy(self.dataset.projs_data)
+        flatfield.normalize_radios(projs)
+        self.check_normalization(projs)
+
+    @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
+    def test_cuda_flatfield(self):
+        d_projs = garray.to_gpu(self.dataset.projs_data)
+        cuda_flatfield = CudaFlatFieldDataUrls(
+            self.dataset.projs_data.shape,
+            self.dataset.flats_urls,
+            self.dataset.darks_urls,
+            radios_indices=self.dataset.projs_idx,
+        )
+        cuda_flatfield.normalize_radios(d_projs)
+        projs = d_projs.get()
+        self.check_normalization(projs)
+
+
+#
+# Another test with more than two flats.
+#
+# Here we have
+#
+#   F_i = i + 2
+#   R_i = i*(F_i - 1) + 1
+#   N_i = (R_i - D)/(F_i - D) = i*(F_i - 1)/( F_i - 1) = i
+#
+
+
+def generate_test_flatfield(n_radios, radio_shape, flat_interval, h5_fname):
+    radios = np.zeros((n_radios,) + radio_shape, "f")
+    dark_data = np.ones(radios.shape[1:], "f")
+    tempdir = mkdtemp(prefix="nabu_")
+    testffname = os.path.join(tempdir, h5_fname)
+    flats = {}
+    flats_urls = {}
+    # F_i = i + 2
+    # R_i = i*(F_i - 1) + 1
+    # N_i = (R_i - D)/(F_i - D) = i*(F_i - 1)/( F_i - 1) = i
+    for i in range(n_radios):
+        f_i = i + 2
+        if (i % flat_interval) == 0:
+            flats["flats_%06d" % i] = np.zeros(radio_shape, "f") + f_i
+            flats_urls[i] = DataUrl(file_path=testffname, data_path=str("/flats/flats_%06d" % i), scheme="silx")
+        radios[i] = i * (f_i - 1) + 1
+    dark = {"dark_0000": dark_data}
+    dicttoh5(flats, testffname, h5path="/flats", mode="w")
+    dicttoh5(dark, testffname, h5path="/dark", mode="a")
+    dark_url = {0: DataUrl(file_path=testffname, data_path="/dark/dark_0000", scheme="silx")}
+    return radios, flats_urls, dark_url
+
+
+@pytest.fixture(scope="class")
+def bootstrap_multiflats(request):
+    cls = request.cls
+
+    n_radios = 50
+    radio_shape = (20, 21)
+    cls.flat_interval = 11
+    h5_fname = "testff.h5"
+
+    radios, flats, dark = generate_test_flatfield(n_radios, radio_shape, cls.flat_interval, h5_fname)
+    cls.radios = radios
+    cls.flats_urls = flats
+    cls.darks_urls = dark
+    cls.expected_results = np.arange(n_radios)
+
+    cls.tol = 5e-4
+    cls.tol_std = 1e-4
+
+    yield
+    # tear down
+    os.remove(dark[0].file_path())
+    os.rmdir(os.path.dirname(dark[0].file_path()))
+
+
+@pytest.mark.usefixtures("bootstrap_multiflats")
+class TestFlatFieldMultiFlat:
+    def check_normalization(self, projs):
+        # Check that each projection is filled with the same values
+        std_projs = np.std(projs, axis=(-2, -1))
+        assert np.max(np.abs(std_projs)) < self.tol_std
+        # Check that the normalized radios are equal to 0, 1, 2, ...
+        stop = (projs.shape[0] // self.flat_interval) * self.flat_interval
+        errs = projs[:stop, 0, 0] - self.expected_results[:stop]
+        assert np.max(np.abs(errs)) < self.tol, "Something wrong with flat-field normalization"
+
+    def test_flatfield(self):
+        flatfield = FlatFieldDataUrls(self.radios.shape, self.flats_urls, self.darks_urls, interpolation="linear")
+        projs = np.copy(self.radios)
+        flatfield.normalize_radios(projs)
+        print(projs[:, 0, 0])
+        self.check_normalization(projs)
+
+    @pytest.mark.skipif(not (__has_pycuda__), reason="Need cuda/pycuda for this test")
+    def test_cuda_flatfield(self):
+        d_projs = garray.to_gpu(self.radios)
+        cuda_flatfield = CudaFlatFieldDataUrls(
+            self.radios.shape,
+            self.flats_urls,
+            self.darks_urls,
+        )
+        cuda_flatfield.normalize_radios(d_projs)
+        projs = d_projs.get()
+        self.check_normalization(projs)

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/preproc/tests/test_paganin.py

@@ -0,0 +1,67 @@
+import pytest
+import numpy as np
+from nabu.preproc.phase import PaganinPhaseRetrieval
+from nabu.testutils import get_data
+from nabu.thirdparty.tomopy_phase import retrieve_phase
+from nabu.cuda.utils import __has_pycuda__, __has_cufft__
+
+if __has_pycuda__:
+    from nabu.preproc.phase_cuda import CudaPaganinPhaseRetrieval
+
+scenarios = [
+    {
+        "distance": 1,
+        "energy": 35,
+        "delta_beta": 1e1,
+        "margin": ((50, 50), (0, 0)),
+    }
+]
+
+
+@pytest.fixture(scope="class", params=scenarios)
+def bootstrap(request):
+    cls = request.cls
+    cls.paganin_config = request.param
+
+    cls.data = get_data("mri_proj_astra.npz")["data"]
+    cls.rtol = 1.1e-6
+    cls.rtol_pag = 5e-3
+    cls.paganin = PaganinPhaseRetrieval(cls.data.shape, **cls.paganin_config)
+
+
+@pytest.mark.usefixtures("bootstrap")
+class TestPaganin:
+    """
+    Test the Paganin phase retrieval.
+    The reference implementation is tomopy.
+    """
+
+    def crop_to_margin(self, data):
+        s0, s1 = self.paganin.shape_inner
+        ((U, _), (L, _)) = self.paganin.margin
+        return data[U : U + s0, L : L + s1]
+
+    def test_paganin(self):
+        data_tomopy = np.atleast_3d(np.copy(self.data)).T
+
+        res_tomopy = retrieve_phase(
+            data_tomopy,
+            pixel_size=self.paganin.pixel_size_micron * 1e-4,
+            dist=self.paganin.distance_cm,
+            energy=self.paganin.energy_kev,
+            alpha=1.0 / (4 * 3.141592**2 * self.paganin.delta_beta),
+        )
+        res_tomopy = self.crop_to_margin(res_tomopy[0].T)
+
+        res = self.paganin.apply_filter(self.data)
+
+        errmax = np.max(np.abs(res - res_tomopy) / np.max(res_tomopy))
+        assert errmax < self.rtol_pag, "Max error is too high"
+
+    @pytest.mark.skipif(not (__has_pycuda__ and __has_cufft__), reason="Need pycuda and scikit-cuda for this test")
+    def test_gpu_paganin(self):
+        gpu_paganin = CudaPaganinPhaseRetrieval(self.data.shape, **self.paganin_config)
+        ref = self.paganin.apply_filter(self.data)
+        res = gpu_paganin.apply_filter(self.data)
+        errmax = np.max(np.abs((res - ref) / np.max(ref)))
+        assert errmax < self.rtol, "Max error is too high"