Detect cropping outside of the image

[multimeric]

Currently if your ROI expands outside of the image, as seen here:

Then the processing fails with:

LogicError: clEnqueueNDRangeKernel failed: INVALID_GLOBAL_WORK_SIZE

Traceback:

---------------------------------------------------------------------------
LogicError                                Traceback (most recent call last)
File ~/Programming/napari_lattice/plugin/napari_lattice/dock_widget.py:172, in LLSZWidget.save(self=<napari_lattice.dock_widget.LLSZWidget object>)
    170 from napari.utils.notifications import show_info
    171 lattice = self._make_model()
--> 172 lattice.save()
        lattice = LatticeData(input_image=<xarray.DataArray (T: 1, C: 1, Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (1, 1, 60, 256, 256) uint16
Dimensions without coordinates: T, C, Z, Y, X, skew=<DeskewDirection.Y: 2>, angle=30.0, physical_pixel_sizes=DefinedPixelSizes(X=0.1499219273, Y=0.1499219273, Z=0.3), derived=DerivedDeskewFields(deskew_vol_shape=(128, 342, 256), deskew_affine_transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8e3473130>), save_dir=PosixPath('/private/tmp'), save_suffix='_deskewed', save_name='membrane_deskewed', save_type=<SaveFileType.h5: 'h5'>, time_range=range(0, 1), channel_range=range(0, 1), deconvolution=None, crop=CropParams(roi_list=[Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))], roi_subset=[0], z_range=(0, 1)), workflow=None)
    173 show_info(f"Deskewing successfuly completed. Results are located in {lattice.save_dir}")

File ~/Programming/napari_lattice/core/lls_core/models/lattice_data.py:463, in LatticeData.save(self=LatticeData(input_image=<xarray.DataArray (T: 1,..., roi_subset=[0], z_range=(0, 1)), workflow=None))
    461     list(self.process_workflow().save())
    462 else:
--> 463     self.process().save_image()
        self = LatticeData(input_image=<xarray.DataArray (T: 1, C: 1, Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (1, 1, 60, 256, 256) uint16
Dimensions without coordinates: T, C, Z, Y, X, skew=<DeskewDirection.Y: 2>, angle=30.0, physical_pixel_sizes=DefinedPixelSizes(X=0.1499219273, Y=0.1499219273, Z=0.3), derived=DerivedDeskewFields(deskew_vol_shape=(128, 342, 256), deskew_affine_transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8e3473130>), save_dir=PosixPath('/private/tmp'), save_suffix='_deskewed', save_name='membrane_deskewed', save_type=<SaveFileType.h5: 'h5'>, time_range=range(0, 1), channel_range=range(0, 1), deconvolution=None, crop=CropParams(roi_list=[Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))], roi_subset=[0], z_range=(0, 1)), workflow=None)

File ~/Programming/napari_lattice/core/lls_core/models/results.py:83, in ImageSlices.save_image(self=ImageSlices(slices=<generator object LatticeData... roi_subset=[0], z_range=(0, 1)), workflow=None)))
     79 """
     80 Saves result slices to disk
     81 """
     82 Writer = self.lattice_data.get_writer()
---> 83 for roi, roi_results in groupby(self.slices, key=lambda it: it.roi_index):
        self.slices = <generator object LatticeData._process_crop at 0x7fb8f36ea490>
        self = ImageSlices(slices=<generator object LatticeData._process_crop at 0x7fb8f36ea490>, lattice_data=LatticeData(input_image=<xarray.DataArray (T: 1, C: 1, Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (1, 1, 60, 256, 256) uint16
Dimensions without coordinates: T, C, Z, Y, X, skew=<DeskewDirection.Y: 2>, angle=30.0, physical_pixel_sizes=DefinedPixelSizes(X=0.1499219273, Y=0.1499219273, Z=0.3), derived=DerivedDeskewFields(deskew_vol_shape=(128, 342, 256), deskew_affine_transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8e3473130>), save_dir=PosixPath('/private/tmp'), save_suffix='_deskewed', save_name='membrane_deskewed', save_type=<SaveFileType.h5: 'h5'>, time_range=range(0, 1), channel_range=range(0, 1), deconvolution=None, crop=CropParams(roi_list=[Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))], roi_subset=[0], z_range=(0, 1)), workflow=None))
     84     writer = Writer(self.lattice_data, roi_index=roi)
     85     for slice in roi_results:

File ~/Programming/napari_lattice/core/lls_core/models/lattice_data.py:354, in LatticeData._process_crop(self=LatticeData(input_image=<xarray.DataArray (T: 1,..., roi_subset=[0], z_range=(0, 1)), workflow=None))
    346 if self.deconvolution is not None:
    347     deconv_args = dict(
    348         num_iter = self.deconvolution.psf_num_iter,
    349         psf = self.deconvolution.psf[slice.channel].to_numpy(),
    350         decon_processing=self.deconvolution.decon_processing
    351     )
    353 yield slice.copy(update={
--> 354     "data": crop_volume_deskew(
        slice = ProcessedSlice(data=<xarray.DataArray (Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (60, 256, 256) uint16
Dimensions without coordinates: Z, Y, X, time_index=0, time=0, channel_index=0, channel=0, roi_index=None)
        slice.data = <xarray.DataArray (Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (60, 256, 256) uint16
Dimensions without coordinates: Z, Y, X
        self = LatticeData(input_image=<xarray.DataArray (T: 1, C: 1, Z: 60, Y: 256, X: 256)>
<class 'numpy.ndarray'> (1, 1, 60, 256, 256) uint16
Dimensions without coordinates: T, C, Z, Y, X, skew=<DeskewDirection.Y: 2>, angle=30.0, physical_pixel_sizes=DefinedPixelSizes(X=0.1499219273, Y=0.1499219273, Z=0.3), derived=DerivedDeskewFields(deskew_vol_shape=(128, 342, 256), deskew_affine_transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8e3473130>), save_dir=PosixPath('/private/tmp'), save_suffix='_deskewed', save_name='membrane_deskewed', save_type=<SaveFileType.h5: 'h5'>, time_range=range(0, 1), channel_range=range(0, 1), deconvolution=None, crop=CropParams(roi_list=[Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))], roi_subset=[0], z_range=(0, 1)), workflow=None)
        roi = Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))
        self.angle = 30.0
        self.crop = CropParams(roi_list=[Roi(top_left=(1234.2218426072347, 1138.9518876459392), top_right=(1234.2218426072347, 2053.5436103361817), bottom_left=(1882.057646179489, 2053.5436103361817), bottom_right=(1882.057646179489, 1138.9518876459392))], roi_subset=[0], z_range=(0, 1))
        self.crop.z_range[0] = 0
        self.crop.z_range = (0, 1)
        self.crop.z_range[1] = 1
        deconv_args = {}
        roi_index = 0
        self.crop.roi_subset[roi_index] = 0
        self.crop.roi_subset = [0]
    355         original_volume=slice.data,
    356         deconvolution=self.deconv_enabled,
    357         get_deskew_and_decon=False,
    358         debug=False,
    359         roi_shape=list(roi),
    360         linear_interpolation=True,
    361         voxel_size_x=self.dx,
    362         voxel_size_y=self.dy,
    363         voxel_size_z=self.dz,
    364         angle_in_degrees=self.angle,
    365         deskewed_volume=self.deskewed_volume,
    366         z_start=self.crop.z_range[0],
    367         z_end=self.crop.z_range[1],
    368         **deconv_args
    369     ),
    370     "roi_index": self.crop.roi_subset[roi_index]
    371 })

File ~/Programming/napari_lattice/core/lls_core/llsz_core.py:257, in crop_volume_deskew(original_volume=<xarray.DataArray (Z: 60, Y: 256, X: 256)>
<clas...6) uint16
Dimensions without coordinates: Z, Y, X, deskewed_volume=dask.array<zeros_like, shape=(128, 342, 256), dt...unksize=(128, 342, 256), chunktype=numpy.ndarray>, roi_shape=[(1234.2218426072347, 1138.9518876459392), (1234.2218426072347, 2053.5436103361817), (1882.057646179489, 2053.5436103361817), (1882.057646179489, 1138.9518876459392)], angle_in_degrees=30.0, voxel_size_x=0.1499219273, voxel_size_y=0.1499219273, voxel_size_z=0.3, z_start=0, z_end=1, debug=False, deconvolution=False, decon_processing=None, psf=None, num_iter=10, linear_interpolation=True, skew_dir=<DeskewDirection.Y: 2>, get_deskew_and_decon=False)
    247         deskewed_no_decon = affine_transform_deskew_3d(
    248             crop_volume,
    249             transform=deskew_transform,
   (...)
    254             deskew_direction=skew_dir,
    255         )
    256 else:
--> 257     deskewed_prelim = affine_transform_deskew_3d(
        crop_volume = <xarray.DataArray (Z: 0, Y: 2, X: 0)>
<class 'numpy.ndarray'> (0, 2, 0) uint16
Dimensions without coordinates: Z, Y, X
        deskew_transform = <pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8f385fbe0>
        angle_in_degrees = 30.0
        voxel_size_x = 0.1499219273
        voxel_size_y = 0.1499219273
        voxel_size_z = 0.3
        skew_dir = <DeskewDirection.Y: 2>
    258         crop_volume,
    259         transform=deskew_transform,
    260         deskewing_angle_in_degrees=angle_in_degrees,
    261         voxel_size_x=voxel_size_x,
    262         voxel_size_y=voxel_size_y,
    263         voxel_size_z=voxel_size_z,
    264         deskew_direction=skew_dir,
    265     )
    267 # The height of deskewed_prelim will be larger than specified shape
    268 # as the coordinates of the ROI are skewed in the original volume
    269 # IF CLIPPING HAPPENS FOR Y_START or Y_END, use difference to calculate offset
    270 if skew_dir == DeskewDirection.Y:

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier0/_plugin_function.py:71, in plugin_function.<locals>.worker_function(*args=(<xarray.DataArray (Z: 0, Y: 2, X: 0)>
<class 'nu...0) uint16
Dimensions without coordinates: Z, Y, X,), **kwargs={'deskew_direction': <DeskewDirection.Y: 2>, 'deskewing_angle_in_degrees': 30.0, 'transform': <pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object>, 'voxel_size_x': 0.1499219273, 'voxel_size_y': 0.1499219273, 'voxel_size_z': 0.3})
     68         bound.arguments[key] = output_creator(*bound.args[:len(sig2.parameters)])
     70 # call the decorated function
---> 71 return function(*bound.args, **bound.kwargs)
        bound = <BoundArguments (source=<class 'numpy.ndarray'> (0, 2, 0) float32, destination=None, transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object at 0x7fb8f385fbe0>, deskewing_angle_in_degrees=30.0, voxel_size_x=0.1499219273, voxel_size_y=0.1499219273, voxel_size_z=0.3, deskew_direction=<DeskewDirection.Y: 2>)>
        function = <function affine_transform_deskew_3d at 0x7fb8e2841f30>

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier8/_affine_transform_deskew_3d.py:105, in affine_transform_deskew_3d(source=<class 'numpy.ndarray'> (0, 2, 0) float32, destination=<class 'numpy.ndarray'> (1, 2, 0) float32, transform=<pyclesperanto_prototype._tier8._AffineTransform3D.AffineTransform3D object>, deskewing_angle_in_degrees=30.0, voxel_size_x=0.1499219273, voxel_size_y=0.1499219273, voxel_size_z=0.3, deskew_direction=<DeskewDirection.Y: 2>)
     93 # pass the shape of the final image, pixel step and precalculated trig
     95 parameters = {
     96     "input": source,
     97     "output": destination,
   (...)
    102     "sintheta": sintheta
    103 }
--> 105 execute(__file__, './affine_transform_' + kernel_suffix + str(len(destination.shape)) + 'd' + '_x.cl',
        destination = <class 'numpy.ndarray'> (1, 2, 0) float32
        kernel_suffix = 'deskew_y_'
        __file__ = '/opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier8/_affine_transform_deskew_3d.py'
        './affine_transform_' + kernel_suffix + str(len(destination.shape)) + 'd' + '_x.cl' = './affine_transform_deskew_y_3d_x.cl'
        destination.shape = (1, 2, 0)
        './affine_transform_' + kernel_suffix + str(len(destination.shape)) + 'd' = './affine_transform_deskew_y_3d'
        './affine_transform_' + kernel_suffix + str(len(destination.shape)) = './affine_transform_deskew_y_3'
        str(len(destination.shape)) = '3'
        './affine_transform_' + kernel_suffix = './affine_transform_deskew_y_'
        len(destination.shape) = 3
        parameters = {'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'pixel_step': 2.0010414, 'tantheta': 0.57735026, 'costheta': 0.8660254, 'sintheta': 0.5}
        'affine_transform_'  + kernel_suffix + str(len(destination.shape)) + 'd' = 'affine_transform_deskew_y_3d'
        'affine_transform_'  + kernel_suffix + str(len(destination.shape)) = 'affine_transform_deskew_y_3'
        'affine_transform_'  + kernel_suffix = 'affine_transform_deskew_y_'
    106         'affine_transform_'  + kernel_suffix + str(len(destination.shape)) + 'd', destination.shape, parameters)
    108 return destination

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier0/_execute.py:35, in execute(anchor='/opt/anaconda3/envs/napari2/lib/python3.10/site-...o_prototype/_tier8/_affine_transform_deskew_3d.py', opencl_kernel_filename='./affine_transform_deskew_y_3d_x.cl', kernel_name='affine_transform_deskew_y_3d', global_size=(1, 2, 0), parameters={'costheta': 0.8660254, 'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'pixel_step': 2.0010414, 'sintheta': 0.5, 'tantheta': 0.57735026}, prog=None, constants=None, image_size_independent_kernel_compilation=None, device=None)
      2 def execute(anchor, opencl_kernel_filename:str, kernel_name:str, global_size, parameters, prog = None, constants = None, image_size_independent_kernel_compilation : bool = None, device = None):
      3     """
      4     Call opencl kernels (.cl files)
      5 
   (...)
     33 
     34     """
---> 35     return Backend.get_instance().get().execute(anchor, opencl_kernel_filename, kernel_name, global_size, parameters, prog, constants, image_size_independent_kernel_compilation, device)
        anchor = '/opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier8/_affine_transform_deskew_3d.py'
        opencl_kernel_filename = './affine_transform_deskew_y_3d_x.cl'
        kernel_name = 'affine_transform_deskew_y_3d'
        global_size = (1, 2, 0)
        parameters = {'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'pixel_step': 2.0010414, 'tantheta': 0.57735026, 'costheta': 0.8660254, 'sintheta': 0.5}
        prog = None
        constants = None
        image_size_independent_kernel_compilation = None
        device = None

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier0/_opencl_backend.py:41, in OpenCLBackend.execute(self=<pyclesperanto_prototype._tier0._opencl_backend.OpenCLBackend object>, anchor='/opt/anaconda3/envs/napari2/lib/python3.10/site-...o_prototype/_tier8/_affine_transform_deskew_3d.py', opencl_kernel_filename='./affine_transform_deskew_y_3d_x.cl', kernel_name='affine_transform_deskew_y_3d', global_size=(1, 2, 0), parameters={'costheta': 0.8660254, 'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'pixel_step': 2.0010414, 'sintheta': 0.5, 'tantheta': 0.57735026}, prog=None, constants=None, image_size_independent_kernel_compilation=None, device=None)
     40 def execute(self, anchor, opencl_kernel_filename, kernel_name, global_size, parameters, prog = None, constants = None, image_size_independent_kernel_compilation : bool = None, device = None):
---> 41     return execute(anchor, opencl_kernel_filename, kernel_name, global_size, parameters, prog, constants, image_size_independent_kernel_compilation, device)
        anchor = '/opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier8/_affine_transform_deskew_3d.py'
        opencl_kernel_filename = './affine_transform_deskew_y_3d_x.cl'
        kernel_name = 'affine_transform_deskew_y_3d'
        global_size = (1, 2, 0)
        parameters = {'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'pixel_step': 2.0010414, 'tantheta': 0.57735026, 'costheta': 0.8660254, 'sintheta': 0.5}
        prog = None
        constants = None
        image_size_independent_kernel_compilation = None
        device = None

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier0/_opencl_execute.py:322, in execute(anchor='/opt/anaconda3/envs/napari2/lib/python3.10/site-...o_prototype/_tier8/_affine_transform_deskew_3d.py', opencl_kernel_filename='./affine_transform_deskew_y_3d_x.cl', kernel_name='affine_transform_deskew_y_3d', global_size=(1, 2, 0), parameters={'costheta': 0.8660254, 'input': <class 'numpy.ndarray'> (0, 2, 0) float32, 'mat': <class 'numpy.ndarray'> (4, 4) float32, 'output': <class 'numpy.ndarray'> (1, 2, 0) float32, 'pixel_step': 2.0010414, 'sintheta': 0.5, 'tantheta': 0.57735026}, prog=<pyclesperanto_prototype._tier0._program.OCLProgram object>, constants=None, image_size_independent_kernel_compilation=True, device=<Apple M2 on Platform: Apple (21 refs)>)
    312     #prog = OCLProgram.from_source("\n".join(defines))
    313 
    314     # Todo: the order of the arguments matters; fix that
    315     # print("Compilation " + opencl_kernel_filename + " took " + str((time.time() - time_stamp) * 1000) + " ms")
    316 else:
    317     warnings.warn(
    318         "The `prog` parameter of pyclesperanto_prototype.execute is deprecated since 0.11.0. It will be removed in 0.12.0.",
    319         DeprecationWarning
    320     )
--> 322 prog.run_kernel(kernel_name, tuple(global_size[::-1]), None, *arguments)
        arguments = [<class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <pyopencl._cl.Buffer object at 0x7fb9044c8900>, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32]
        prog = <pyclesperanto_prototype._tier0._program.OCLProgram object at 0x7fb8f32ad660>
        kernel_name = 'affine_transform_deskew_y_3d'
        tuple(global_size[::-1]) = (0, 2, 1)
        global_size[::-1] = (0, 2, 1)
        global_size = (1, 2, 0)
    324 return prog

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyclesperanto_prototype/_tier0/_program.py:34, in OCLProgram.run_kernel(self=<pyclesperanto_prototype._tier0._program.OCLProgram object>, name='affine_transform_deskew_y_3d', global_size=(0, 2, 1), local_size=None, *args=(<class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <pyopencl._cl.Buffer object>, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32), **kwargs={})
     31 if name not in self._kernel_dict:
     32     self._kernel_dict[name] = getattr(self, name)
---> 34 self._kernel_dict[name](
        name = 'affine_transform_deskew_y_3d'
        self._kernel_dict = {'affine_transform_deskew_y_3d': <pyopencl._cl.Kernel object at 0x7fb8f32fe250>}
        self._kernel_dict[name] = <pyopencl._cl.Kernel object at 0x7fb8f32fe250>
        self = <pyclesperanto_prototype._tier0._program.OCLProgram object at 0x7fb8f32ad660>
        self._dev.queue = <pyopencl._cl.CommandQueue object at 0x7fb8e2865e90>
        global_size = (0, 2, 1)
        local_size = None
        self._dev = <Apple M2 on Platform: Apple (21 refs)>
        args = (<class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <pyopencl._cl.Buffer object at 0x7fb9044c8900>, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32)
        kwargs = {}
     35     self._dev.queue, global_size, local_size, *args, **kwargs
     36 )
     37 if OCLProgram._wait_for_kernel_finish:
     38     self._dev.queue.finish()

File /opt/anaconda3/envs/napari2/lib/python3.10/site-packages/pyopencl/__init__.py:901, in _add_functionality.<locals>.kernel_call(self=<pyopencl._cl.Kernel object>, queue=<pyopencl._cl.CommandQueue object>, global_size=(0, 2, 1), local_size=None, *args=(<class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <pyopencl._cl.Buffer object>, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32), **kwargs={})
    895 def kernel_call(self, queue, global_size, local_size, *args, **kwargs):
    896     # __call__ can't be overridden directly, so we need this
    897     # trampoline hack.
    898 
    899     # Note: This is only used for the generic __call__, before
    900     # kernel_set_scalar_arg_dtypes is called.
--> 901     return self._enqueue(self, queue, global_size, local_size, *args, **kwargs)
        self._enqueue = <function enqueue_knl_affine_transform_deskew_y_3d at 0x7fb8f3263520>
        self = <pyopencl._cl.Kernel object at 0x7fb8f32fe250>
        queue = <pyopencl._cl.CommandQueue object at 0x7fb8e2865e90>
        global_size = (0, 2, 1)
        local_size = None
        args = (<class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, None, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <class 'numpy.ndarray'> (1,) int32, <pyopencl._cl.Buffer object at 0x7fb9044c8900>, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32, <class 'numpy.ndarray'> (1,) float32)
        kwargs = {}

File <pyopencl invoker for 'affine_transform_deskew_y_3d'>:8, in enqueue_knl_affine_transform_deskew_y_3d(self=<pyopencl._cl.Kernel object>, queue=<pyopencl._cl.CommandQueue object>, global_size=(0, 2, 1), local_size=None, arg0=<class 'numpy.ndarray'> (1,) int32, arg1=<class 'numpy.ndarray'> (1,) int32, arg2=<class 'numpy.ndarray'> (1,) int32, arg3=None, arg4=<class 'numpy.ndarray'> (1,) int32, arg5=<class 'numpy.ndarray'> (1,) int32, arg6=<class 'numpy.ndarray'> (1,) int32, arg7=None, arg8=<class 'numpy.ndarray'> (1,) int32, arg9=<class 'numpy.ndarray'> (1,) int32, arg10=<class 'numpy.ndarray'> (1,) int32, arg11=<pyopencl._cl.Buffer object>, arg12=<class 'numpy.ndarray'> (1,) float32, arg13=<class 'numpy.ndarray'> (1,) float32, arg14=<class 'numpy.ndarray'> (1,) float32, arg15=<class 'numpy.ndarray'> (1,) float32, global_offset=None, g_times_l=False, allow_empty_ndrange=False, wait_for=None)

LogicError: clEnqueueNDRangeKernel failed: INVALID_GLOBAL_WORK_SIZE

This should be detected using a new validator on the LatticeData model.

[pr4deepr]

The code here should take care of it

https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/blob/master/core%2Flls_core%2Fllsz_core.py#L160

Assuming the coordinates get passed in pixels instead of microns?

[multimeric]

I don't think the scale is an issue here. I'll have to investigate why it doesn't get clipped appropriately.

[pr4deepr]

I remember testing this in napari.
Could you run this using cli only? Although it will have to be an ROI manager file from Fiji.

[multimeric]

Hmm actually this might be a bug in #91. Let me know if you can work out the cause, because I thought I was correctly scaling it by dy:

napari_lattice/plugin/napari_lattice/fields.py

Lines 492 to 493 in 8146b9a

	for shape in self.shapes.shapes.value:
	rois.append(Roi.from_array(shape.get_array() / deskew.dy))

[multimeric]

Closing as I haven't been able to reproduce this recently.