nabu 2024.1.1__tar.gz → 2024.1.3__tar.gz

{nabu-2024.1.1/nabu.egg-info → nabu-2024.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.1
+Version: 2024.1.3
 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>
@@ -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>=2.0.0a7
+Requires-Dist: tomoscan>=2.0.4
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

nabu-2024.1.3/doc/doc_config.py

@@ -0,0 +1,32 @@
+#!/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-2024.1.1 → nabu-2024.1.3}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.1.1"
+__version__ = "2024.1.3"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/app/cast_volume.py

@@ -228,11 +228,20 @@ def main(argv=None):
 
     # get rescale_min_percentile and rescale_min_percentile
     rescale_min_percentile = options.rescale_min_percentile
+
+    def clean_percentiles_str(percentile):
+        # remove ' char
+        percentile = percentile.rstrip("'").lstrip("'")
+        # remove " char
+        percentile = percentile.rstrip('"').lstrip('"')
+        # remove % char
+        return percentile.rstrip("%")
+
     if isinstance(rescale_min_percentile, str):
-        rescale_min_percentile = float(rescale_min_percentile.rstrip("%"))
+        rescale_min_percentile = float(clean_percentiles_str(rescale_min_percentile))
     rescale_max_percentile = options.rescale_max_percentile
     if isinstance(rescale_min_percentile, str):
-        rescale_max_percentile = float(rescale_max_percentile.rstrip("%"))
+        rescale_max_percentile = float(clean_percentiles_str(rescale_max_percentile))
     assert rescale_min_percentile is not None, "rescale_min_percentile should be an int"
     assert rescale_max_percentile is not None, "rescale_max_percentile should be an int"
 

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/app/multicor.py

@@ -60,12 +60,12 @@ def main():
     cors = get_user_cors(args["cor"])
 
     all_recs = []
+    rec_instance = pipeline.reconstruction
 
     for cor in cors:
         # Re-configure with new CoR
         pipeline.processing_options["reconstruction"]["rotation_axis_position"] = cor
         pipeline.processing_options["save"]["file_prefix"] = file_prefix + "_%.03f" % cor
-        pipeline.reconstruction.reset_rot_center(cor)
         pipeline._init_writer(create_subfolder=False, single_output_file_initialized=False)
 
         # Get sinogram into contiguous array
@@ -73,8 +73,30 @@ def main():
         # For now: transfer to host... not optimal
         sino = pipeline._d_radios[:, pipeline._d_radios.shape[1] // 2, :].get()  # pylint: disable=E1136
 
+        if pipeline.process_config.do_halftomo:
+            # re-initialize FBP object, because in half-tomography the output slice size is a function of CoR
+            options = pipeline.processing_options["reconstruction"]
+            rec_instance = pipeline.FBPClass(
+                sino.shape,
+                angles=options["angles"],
+                rot_center=cor,
+                filter_name=options["fbp_filter_type"] or "none",
+                halftomo=options["enable_halftomo"],
+                # slice_roi=self.process_config.rec_roi,
+                padding_mode=options["padding_type"],
+                extra_options={
+                    "scale_factor": 1.0 / options["voxel_size_cm"][0],
+                    "axis_correction": options["axis_correction"],
+                    "centered_axis": options["centered_axis"],
+                    "clip_outer_circle": options["clip_outer_circle"],
+                    "filter_cutoff": options["fbp_filter_cutoff"],
+                },
+            )
+        else:
+            pipeline.reconstruction.reset_rot_center(cor)
+
         # Run reconstruction
-        rec = pipeline.reconstruction.fbp(sino)
+        rec = rec_instance.fbp(sino)
         # if return_all_recs:
         # all_recs.append(rec)
         rec_3D = view_as_images_stack(rec)  # writer wants 3D data

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/io/cast_volume.py

@@ -74,7 +74,7 @@ def get_default_output_volume(
                 volume_basename=input_volume.get_volume_basename(),
             )
         else:
-            raise NotImplementedError
+            raise NotImplementedError(f"output volume format {output_type} is not handled")
     elif isinstance(input_volume, (HDF5Volume, MultiTIFFVolume)):
         if output_type == "hdf5":
             data_file_parent_path, data_file_name = os.path.split(input_volume.data_url.file_path())
@@ -121,9 +121,9 @@ def get_default_output_volume(
                 )
             )
         else:
-            raise NotImplementedError
+            raise NotImplementedError(f"output volume format {output_type} is not handled")
     else:
-        raise NotImplementedError
+        raise NotImplementedError(f"input volume format {input_volume} is not handled")
 
 
 def cast_volume(

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/io/utils.py

@@ -201,7 +201,7 @@ class EntryReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(self._url.file_path(), mode="r")
         if self._url.data_path() == "":
             entry = self._file_handler
         else:
@@ -215,7 +215,7 @@ class DatasetReader(_BaseReader):
     """Context manager used to read a bliss node"""
 
     def __enter__(self):
-        self._file_handler = HDF5File(filename=self._url.file_path(), mode="r")
+        self._file_handler = HDF5File(self._url.file_path(), mode="r")
         entry = self._file_handler[self._url.data_path()]
         if not isinstance(entry, h5py.Dataset):
             raise ValueError("Data path ({}) should point to a dataset (h5py.Dataset)".format(self._url.path()))

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/reconstruction/rings_cuda.py

@@ -174,10 +174,15 @@ class CudaMunchDeringer(MunchDeringer):
             self._fft_plans[level].ifft(d_coeffs_f, output=d_coeffs)
 
     def _destripe_2D(self, d_sino, output):
+        if not (d_sino.flags.c_contiguous):
+            sino = self.cuda_processing.allocate_array("_d_sino", d_sino.shape, np.float32)
+            sino[:] = d_sino[:]
+        else:
+            sino = d_sino
         if self.padding is not None:
-            d_sino = self.padder.pad(d_sino)
+            sino = self.padder.pad(sino)
         # set the "image" for DWT (memcpy D2D)
-        self._d_sino.set(d_sino)
+        self._d_sino.set(sino)
         # perform forward DWT
         self.cudwt.forward()
         for i in range(self.cudwt.levels):
@@ -256,9 +261,10 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
             filename=get_cuda_srcfile("normalization.cu"),
             signature="PPiii",
         )
-        self._mean_kernel_block = (32, 1, 32)
-        self._mean_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[::-1], self._mean_kernel_block)]
-        self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(self.n_z)]
+        self._mean_kernel_block = (32, 1, 1)
+        self._mean_kernel_grid = [updiv(self.sinos_shape[-1], self._mean_kernel_block[0]), 1, 1]
+        self._mean_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
+
         self._mean_kernel_kwargs = {
             "grid": self._mean_kernel_grid,
             "block": self._mean_kernel_block,
@@ -270,9 +276,11 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
             signature="PPiii",
             options=["-DGENERIC_OP=%d" % (3 if self.mode == "divide" else 1)],
         )
-        self._op_kernel_block = (16, 16, 4)
-        self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[::-1], self._op_kernel_block)]
-        self._op_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(self.n_z)]
+        self._op_kernel_block = (16, 16, 1)
+        self._op_kernel_grid = [updiv(a, b) for a, b in zip(self.sinos_shape[1:][::-1], self._op_kernel_block[:-1])] + [
+            1
+        ]
+        self._op_kernel_args = [self.d_sino_profile, np.int32(self.n_x), np.int32(self.n_angles), np.int32(1)]
         self._op_kernel_kwargs = {
             "grid": self._op_kernel_grid,
             "block": self._op_kernel_block,
@@ -312,9 +320,16 @@ class CudaSinoMeanDeringer(SinoMeanDeringer):
         if output is not None:
             raise NotImplementedError
         #
-        self._mean_kernel(sino, *self._mean_kernel_args, **self._mean_kernel_kwargs)
+        if not (sino.flags.c_contiguous):
+            d_sino = self.processing.allocate_array("d_sino", sino.shape, np.float32)
+            d_sino[:] = sino[:]
+        else:
+            d_sino = sino
+        self._mean_kernel(d_sino, *self._mean_kernel_args, **self._mean_kernel_kwargs)
         self._apply_filter(self.d_sino_profile)
-        self._op_kernel(sino, *self._op_kernel_args, **self._op_kernel_kwargs)
+        self._op_kernel(d_sino, *self._op_kernel_args, **self._op_kernel_kwargs)
+        if not (sino.flags.c_contiguous):
+            sino[:] = self.processing.d_sino[:]
         return sino
 
     def remove_rings_sinograms(self, sinograms):

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/stitching/tests/test_z_stitching.py

@@ -726,7 +726,6 @@ def test_get_overlap_areas():
 
 def test_frame_flip(tmp_path):
     """check it with some NXtomo fliped"""
-    pytest.skip(reason="Broken test")
     ref_frame_width = 280
     n_proj = 10
     raw_frame_width = 100

{nabu-2024.1.1 → nabu-2024.1.3}/nabu/stitching/z_stitching.py

@@ -1258,7 +1258,7 @@ class PreProcessZStitcher(ZStitcher):
 
         output_dtype = get_output_data_type()
         # append frames ("instrument/detactor/data" dataset)
-        with HDF5File(filename=self.configuration.output_file_path, mode="a") as h5f:
+        with HDF5File(self.configuration.output_file_path, mode="a") as h5f:
             # note: nx_tomo.save already handles the possible overwrite conflict by removing
             # self.configuration.output_file_path or raising an error
 
@@ -1834,7 +1834,7 @@ class PostProcessZStitcher(ZStitcher):
         def __enter__(self):
             # handle the specific case of HDF5. Goal: avoid getting the full stitched volume in memory
             if isinstance(self._volume, HDF5Volume):
-                self.__file_handler = HDF5File(filename=self._volume.data_url.file_path(), mode="a")
+                self.__file_handler = HDF5File(self._volume.data_url.file_path(), mode="a")
                 # if need to delete an existing dataset
                 if self._volume.overwrite and self._volume.data_path in self.__file_handler:
                     try:
@@ -1902,7 +1902,7 @@ class PostProcessZStitcher(ZStitcher):
                     if volume.data is not None:
                         data = volume.data
                     elif isinstance(volume, HDF5Volume):
-                        file_handler = HDF5File(filename=volume.data_url.file_path(), mode="r")
+                        file_handler = HDF5File(volume.data_url.file_path(), mode="r")
                         dataset = file_handler[volume.data_url.data_path()]
                         data = dataset
                         self.__file_handlers.append(file_handler)

{nabu-2024.1.1 → nabu-2024.1.3/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.1.1
+Version: 2024.1.3
 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>
@@ -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>=2.0.0a7
+Requires-Dist: tomoscan>=2.0.4
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile

{nabu-2024.1.1 → nabu-2024.1.3}/nabu.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ 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
@@ -295,4 +296,35 @@ nabu/thirdparty/algotom_convert_sino.py
 nabu/thirdparty/pore3d_deringer_munch.py
 nabu/thirdparty/tomocupy_remove_stripe.py
 nabu/thirdparty/tomopy_phase.py
-nabu/thirdparty/tomwer_load_flats_darks.py
+nabu/thirdparty/tomwer_load_flats_darks.py
+sandbox/align_test.py
+sandbox/app.py
+sandbox/binning_cython.py
+sandbox/circ_sm.py
+sandbox/composite_image.py
+sandbox/convert_id15.py
+sandbox/do_test_ctf.py
+sandbox/esrf_envs.py
+sandbox/fbp_polar.py
+sandbox/fbp_tilt.py
+sandbox/interleaved.py
+sandbox/interp_sinos_halftomo.py
+sandbox/linear_interp.py
+sandbox/merge_recs.py
+sandbox/moduleutils.py
+sandbox/nbreconstruct.py
+sandbox/pag_margin.py
+sandbox/parse.py
+sandbox/plot.py
+sandbox/proj3D.py
+sandbox/rec_bm05.py
+sandbox/rec_thread.py
+sandbox/shift_bilinear2.py
+sandbox/sinotilt.py
+sandbox/sysutils.py
+sandbox/test_mp_queue.py
+sandbox/tilt.py
+sandbox/utils.py
+sandbox/vo.py
+sandbox/workers.py
+sandbox/xrdrec_pyFAI_data.py

{nabu-2024.1.1 → nabu-2024.1.3}/nabu.egg-info/requires.txt

@@ -2,7 +2,7 @@ numpy>1.9.0
 scipy
 h5py>=3.0
 silx>=0.15.0
-tomoscan>=2.0.0a7
+tomoscan>=2.0.4
 psutil
 pytest
 tifffile

{nabu-2024.1.1 → nabu-2024.1.3}/pyproject.toml

@@ -53,7 +53,7 @@ dependencies = [
     "scipy",
     "h5py>=3.0",
     "silx >= 0.15.0",
-    "tomoscan >= 2.0.0a7",
+    "tomoscan >= 2.0.4",
     "psutil",
     "pytest",
     "tifffile",

nabu-2024.1.3/sandbox/align_test.py

@@ -0,0 +1,61 @@
+import numpy as np
+from nabu.estimation.translation import DetectorTranslationAlongBeam
+from tomoscan.io import HDF5File
+
+
+def get_data(fname, h5_paths):
+    with HDF5File(fname, "r") as f:
+        align_data = f[h5_paths["align_data"]][()]
+        dark = f[h5_paths["dark"]][0]
+        pixel_size_um = f[h5_paths["pixel_size"]][()]
+        positions_mm = f[h5_paths["positions"]][()]
+
+    # Dark subtraction
+    align_data = align_data - dark.astype("f")
+
+    return align_data, pixel_size_um, positions_mm
+
+
+
+def get_alignment(align_data, pixel_size_um, positions_mm, plot=True):
+
+    tr_calc = DetectorTranslationAlongBeam()
+    if plot == True:
+        tr_calc.verbose=True
+
+    shifts_v, shifts_h = tr_calc.find_shift(align_data, positions_mm)
+
+    # pixel_size is in microns, motor position is in mm
+    tilt_v_deg = np.rad2deg(np.arctan(shifts_v * pixel_size_um / 1e3))
+    tilt_h_deg = np.rad2deg(np.arctan(shifts_h * pixel_size_um / 1e3))
+    print (f"\nVertical tilt  to be applied in deg (thy): {tilt_v_deg}")
+    print (f"Horizontal tilt to be applied in deg (thz): {tilt_h_deg}\n")
+
+    return align_data, shifts_v, shifts_h, positions_mm
+
+
+
+
+
+
+if __name__ == "__main__":
+    fname = "/data/id19/inhouse/id192201/id19/sample/sample_0001/sample_0001.h5"
+    h5_paths = {
+        "align_data": "11.1/measurement/pcolinux",
+        "dark": "12.1/measurement/pcolinux",
+        "pixel_size": "11.1/instrument/pcolinux/x_pixel_size",
+        "positions": "11.1/measurement/hrxc"
+    }
+    align_data, pixel_size_um, positions_mm = get_data(fname, h5_paths)
+    # align_data, shifts_v, shifts_h, positions_mm = get_alignment(align_data, pixel_size_um, positions_mm)
+
+    D = DetectorTranslationAlongBeam()
+    D. verbose = True
+    sv, sh = D.find_shift(align_data, positions_mm)
+    D.verbose = False
+    sv, sh = D.find_shift(align_data, positions_mm)
+    D.verbose = True
+    sv, sh = D.find_shift(align_data, positions_mm)
+
+
+

nabu-2024.1.3/sandbox/app.py

@@ -0,0 +1,123 @@
+from time import sleep
+import pycuda.autoinit
+import pycuda.gpuarray as garray
+from nabu.resources.processconfig import ProcessConfig
+from nabu.resources.tasks import build_processing_steps
+
+from nabu.app.logger import Logger
+
+from nabu.app.chunkreader import ChunkReaderComponent
+from nabu.app.flatfield import FlatFieldComponent
+from nabu.app.phase import PhaseRetrievalComponent
+from nabu.app.opmap import NegativeLogComponent
+from nabu.app.ccdfilter import CCDFilterComponent
+from nabu.app.unsharp import UnsharpMaskComponent
+from nabu.app.reconstructor import ReconstructorComponent
+
+
+if __name__ == "__main__":
+
+    conf = ProcessConfig("/home/pierre/workspace/data/nabu.conf")
+    steps, options = build_processing_steps(conf)
+    dataset_infos = conf.dataset_infos
+    SUB_REGION = (None, None, None, 50)
+
+    logger = Logger("nabu_processing", console=True)
+
+    # Read chunk
+    options["read_chunk"]["sub_region"] = SUB_REGION
+    options["read_chunk"]["convert_float"] = True
+    Ch = ChunkReaderComponent(options["read_chunk"], dataset_infos, logger=logger)
+    Ch.execute()
+    radios = Ch.chunk_reader.files_data
+    d_radios = garray.to_gpu(radios)
+
+    # Flat-field
+    options["flatfield"]["sub_region"] = SUB_REGION
+    options["flatfield"]["use_opencl"] = False
+    options["flatfield"]["use_cuda"] = True
+    F = FlatFieldComponent(d_radios, options["flatfield"], dataset_infos, logger=logger)
+    F.execute()
+
+    # CCD filter
+    options["ccd_correction"]["use_cuda"] = True
+    options["ccd_correction"]["use_opencl"] = False
+    CCD = CCDFilterComponent(d_radios, options["ccd_correction"], dataset_infos, logger=logger)
+    CCD.execute()
+
+
+    # Phase retrieval
+    options["phase"]["use_cuda"] = True
+    options["phase"]["use_opencl"] = False
+    P = PhaseRetrievalComponent(radios[0].shape, options["phase"], dataset_infos, logger=logger)
+    P.execute(d_radios)
+
+    # Unsharp
+    # ~ options["unsharp_mask"]["use_cuda"] = True
+    # ~ options["unsharp_mask"]["use_opencl"] = False
+    # ~ U = UnsharpMaskComponent(radios[0].shape, options["unsharp_mask"], dataset_infos, logger=logger)
+    # ~ U.execute(d_radios)
+
+    # -log()
+    options["take_log"]["use_cuda"] = True
+    options["take_log"]["use_opencl"] = False
+    L = NegativeLogComponent(d_radios, options["take_log"], dataset_infos, logger=logger)
+    L.execute()
+
+
+    # Test
+    # ~ from spire.utils import ims
+    # ~ r = d_radios.get()
+    # ~ ims(r[:, 10, :])
+
+
+    # Reconstruction
+    options["reconstruction"]["use_cuda"] = True
+
+    # Test ...
+    if 1:
+        options["reconstruction"]["start_x"] = 100
+        options["reconstruction"]["end_x"] = -100
+        options["reconstruction"]["start_y"] = 100
+        options["reconstruction"]["end_y"] = -100
+        options["reconstruction"]["start_z"] = 0
+        options["reconstruction"]["end_z"] = SUB_REGION[-1]-1
+        d_rec = garray.zeros((50, 1849, 1849), "f") # y
+    #
+    else:
+        d_rec = garray.zeros((SUB_REGION[-1], 2048, 2048), "f")
+    R = ReconstructorComponent(d_radios.shape, options["reconstruction"], dataset_infos, logger=logger)
+    R.execute(d_radios, output=d_rec)
+
+
+    # Write to file
+    rec = d_rec.get()
+    import numpy as np
+    np.save("/home/pierre/tmp/crayon/recs_nabu_vertical.npy", rec)
+
+    """from nabu.reconstruction.reconstructor_cuda import CudaReconstructor
+    R = CudaReconstructor(
+        radios.shape,
+        [0, 1],
+        vol_type="projections",
+        extra_options={"padding_mode": conf.nabu_config["reconstruction"]["padding_type"]}
+    )
+    d_recs = garray.zeros((1, 2048, 2048), "f")
+    R.reconstruct(d_radios, output=d_recs)
+    recs = d_recs.get()
+    ims(recs[0], cmap="gray")
+    # save
+    import numpy as np
+    np.save("/tmp/rec0.npy", recs[0])
+    """
+
+
+"""
+Notes
+  - If the cuda backend is used at step N, it should also be used at step N+1,
+
+
+otherwise we have to get() the data
+
+"""
+

nabu-2024.1.3/sandbox/binning_cython.py

@@ -0,0 +1,37 @@
+%%cython --compile-args=-fopenmp --link-args=-fopenmp -a
+#%%cython -a
+#cython: embedsignature=True, language_level=3, binding=True
+#cython: boundscheck=False, wraparound=False, cdivision=True, initializedcheck=False,
+## This is for developping:
+## cython: profile=True, warn.undeclared=True, warn.unused=True, warn.unused_result=False, warn.unused_arg=True
+
+import numpy as np
+from cython.parallel import prange
+"""
+def bin2_cython(float[:, ::1] img):
+    cdef:
+        float[:, ::1] res
+        int i, j, Ny, Nx
+          
+    shp = img.shape
+    Ny, Nx = (img.shape[0]//2, img.shape[1]//2)
+    res = np.zeros((Ny, Nx), dtype="f")
+    for i in prange(Ny, nogil=True): 
+        for j in range(Nx):
+            res[i, j] = 0.25 * (img[2*i, 2*j] + img[2*i+1, 2*j] + img[2*i, 2*j+1] + img[2*i+1, 2*j+1])
+    return np.asarray(res)
+"""
+
+
+def bin2_cython(unsigned short[:, ::1] img):
+    cdef:
+        float[:, ::1] res
+        int i, j, Ny, Nx
+          
+    shp = img.shape
+    Ny, Nx = (img.shape[0]//2, img.shape[1]//2)
+    res = np.zeros((Ny, Nx), dtype="f")
+    for i in prange(Ny, nogil=True): 
+        for j in range(Nx):
+            res[i, j] = 0.25 * (img[2*i, 2*j] + img[2*i+1, 2*j] + img[2*i, 2*j+1] + img[2*i+1, 2*j+1])
+    return np.asarray(res)