nabu 2024.2.4__py3-none-any.whl → 2025.1.0.dev4__py3-none-any.whl

nabu/io/writer.py

@@ -13,7 +13,6 @@ try:
 except:
     from h5py import File as HDF5File
 from tomoscan.esrf import RawVolume
-from tomoscan.esrf.volume.jp2kvolume import has_glymur as __have_jp2k__
 from .. import version as nabu_version
 from ..utils import merged_shape
 from .utils import convert_dict_values
@@ -183,7 +182,7 @@ class NXVolVolume(NXProcessWriter):
         volume_basename = file_prefix = kwargs.get("volume_basename", None)
         start_index = kwargs.get("start_index", None)
         overwrite = kwargs.get("overwrite", False)
-        data_path = entry = kwargs.get("data_path", None)
+        entry = kwargs.get("data_path", None)
         self._process_name = kwargs.get("process_name", "reconstruction")
         if any([param is None for param in [folder, volume_basename, start_index, entry]]):
             raise ValueError("Need the following parameters: folder, volume_basename, start_index, data_path")

nabu/misc/fftshift.py

@@ -1,4 +1,4 @@
-from ..processing.fftshift import *
+from ..processing.fftshift import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/fourier_filters.py

@@ -1,7 +1,7 @@
-# -*- coding: utf-8 -*-
 """
 Fourier filters.
 """
+
 from functools import lru_cache
 import numpy as np
 import scipy.special as spspe

nabu/misc/histogram.py

@@ -1,4 +1,4 @@
-from ..processing.histogram import *
+from ..processing.histogram import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/histogram_cuda.py

@@ -1,4 +1,4 @@
-from ..processing.histogram_cuda import *
+from ..processing.histogram_cuda import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/padding_base.py

@@ -1,4 +1,4 @@
-from ..processing.padding_base import *
+from ..processing.padding_base import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/rotation.py

@@ -1,4 +1,4 @@
-from ..processing.rotation import *
+from ..processing.rotation import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/rotation_cuda.py

@@ -1,4 +1,4 @@
-from ..processing.rotation_cuda import *
+from ..processing.rotation_cuda import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/tests/test_binning.py

@@ -1,7 +1,7 @@
 from itertools import product
 import numpy as np
 import pytest
-from nabu.misc.binning import *
+from nabu.misc.binning import binning
 
 
 @pytest.fixture(scope="class")

nabu/misc/transpose.py

@@ -1,4 +1,4 @@
-from ..processing.transpose import *
+from ..processing.transpose import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/unsharp.py

@@ -1,4 +1,4 @@
-from ..processing.unsharp import *
+from ..processing.unsharp import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning("nabu.misc.unsharp has been moved to nabu.processing.unsharp", do_print=True, func_name="unsharp")

nabu/misc/unsharp_cuda.py

@@ -1,4 +1,4 @@
-from ..processing.unsharp_cuda import *
+from ..processing.unsharp_cuda import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/unsharp_opencl.py

@@ -1,4 +1,4 @@
-from ..processing.unsharp_opencl import *
+from ..processing.unsharp_opencl import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/misc/utils.py

@@ -41,7 +41,7 @@ def psnr(img1, img2):
 #
 
 
-class ConvolutionInfos(object):
+class ConvolutionInfos:
     allowed_axes = {
         "1D": [None],
         "separable_2D_1D_2D": [None, (0, 1), (1, 0)],

nabu/opencl/fft.py

@@ -1,4 +1,4 @@
-from ..processing.fft_opencl import *
+from ..processing.fft_opencl import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/opencl/padding.py

@@ -1,4 +1,4 @@
-from ..processing.padding_opencl import *
+from ..processing.padding_opencl import *  # noqa: F403
 from ..utils import deprecation_warning
 
 deprecation_warning(

nabu/opencl/utils.py

@@ -1,5 +1,5 @@
 import numpy as np
-from ..utils import check_supported
+from ..utils import check_supported, first_generator_item
 
 try:
     import pyopencl as cl
@@ -138,11 +138,11 @@ def collect_opencl_gpus():
     Return a dictionary of platforms and brief description of each OpenCL-compatible
     GPU with a few fields
     """
-    gpus, error_msg = detect_opencl_gpus()
+    gpus_detected, error_msg = detect_opencl_gpus()
     if error_msg is not None:
         return None
     opencl_gpus = {}
-    for platform, gpus in gpus.items():
+    for platform, gpus in gpus_detected.items():
         for gpu_id, gpu in gpus.items():
             if platform not in opencl_gpus:
                 opencl_gpus[platform] = {}
@@ -215,22 +215,22 @@ def pick_opencl_cpu_platform(opencl_cpus):
         raise ValueError("No CPU to pick")
     name2device = {}
     for platform, devices in opencl_cpus.items():
-        for device_id, device_desc in devices.items():
+        for device_id, device_desc in devices.items():  # noqa: PERF102
             name2device.setdefault(device_desc["name"], [])
             name2device[device_desc["name"]].append(platform)
     if len(name2device) > 1:
         raise ValueError("Expected at most one CPU but got %d: %s" % (len(name2device), list(name2device.keys())))
-    cpu_name = list(name2device.keys())[0]
+    cpu_name = first_generator_item(name2device.keys())
     platforms = name2device[cpu_name]
     # Several platforms for the same CPU
     res = opencl_cpus[platforms[0]]
-    if len(platforms) > 1:
+    if len(platforms) > 1:  # noqa: SIM102
         if "intel" in cpu_name.lower():
             for platform in platforms:
                 if "intel" in platform.lower():
                     res = opencl_cpus[platform]
     #
-    return res[list(res.keys())[0]]
+    return res[first_generator_item(res.keys())]
 
 
 def allocate_texture(ctx, shape, support_1D=False):
@@ -289,4 +289,4 @@ def copy_to_texture(queue, dst_texture, src_array, dtype=np.float32):
             src_array = np.ascontiguousarray(src_array, dtype=dtype)
         return cl.enqueue_copy(queue, dst_texture, src_array, origin=(0, 0), region=shape[::-1])
     else:
-        raise ValueError("Unknown source array type")
+        raise TypeError("Unknown source array type")

nabu/pipeline/config.py

@@ -156,7 +156,7 @@ def _extract_nabuconfig_section(section, default_config):
 
 def _extract_nabuconfig_keyvals(default_config):
     res = {}
-    for section in default_config.keys():
+    for section in default_config:
         res[section] = _extract_nabuconfig_section(section, default_config)
     return res
 
@@ -257,7 +257,7 @@ def overwrite_config(conf, overwritten_params):
         if section not in conf:
             raise ValueError("Unknown section %s" % section)
         current_section = conf[section]
-        for key in params.keys():
+        for key in params:
             if key not in current_section:
                 raise ValueError("Unknown parameter '%s' in section '%s'" % (key, section))
             conf[section][key] = overwritten_params[section][key]

nabu/pipeline/config_validators.py

@@ -1,8 +1,9 @@
+# ruff: noqa: F405
 import os
 
 path = os.path
 from ..utils import check_supported, is_writeable
-from .params import *
+from .params import *  # noqa: F403
 
 """
 A validator is a function with
@@ -310,7 +311,7 @@ def optional_nonzero_float_validator(val):
         assert error is None, "Invalid number"
     else:
         val_float = None
-    if val_float is not None:
+    if val_float is not None:  # noqa: SIM102
         if abs(val_float) < 1e-6:
             val_float = None
     return val_float
@@ -323,7 +324,7 @@ def optional_tuple_of_floats_validator(val):
     err_msg = "Expected a tuple of two numbers, but got %s" % val
     try:
         res = tuple(float(x) for x in val.strip("()").split(","))
-    except Exception as exc:
+    except Exception:
         raise ValueError(err_msg)
     if len(res) != 2:
         raise ValueError(err_msg)

nabu/pipeline/datadump.py

@@ -126,7 +126,7 @@ class DataDumpManager:
         read_opts = self.processing_options["read_chunk"]
         if read_opts.get("process_file", None) is None:
             return None
-        dump_start_z, dump_end_z = read_opts["dump_start_z"], read_opts["dump_end_z"]
+        dump_start_z, dump_end_z = read_opts["dump_start_z"], read_opts["dump_end_z"]  # noqa: F841
         relative_start_z = self.z_min - dump_start_z
         relative_end_z = relative_start_z + self.delta_z
         # When using binning, every step after "read" results in smaller-sized data.
@@ -139,7 +139,7 @@ class DataDumpManager:
 
     def _check_resume_from_step(self):
         read_opts = self.processing_options["read_chunk"]
-        expected_radios_shape = get_hdf5_dataset_shape(
+        expected_radios_shape = get_hdf5_dataset_shape(  # noqa: F841
             read_opts["process_file"],
             read_opts["process_h5_path"],
             sub_region=self.get_read_dump_subregion(),
@@ -151,7 +151,7 @@ class DataDumpManager:
             return
         writer = self.data_dump[step_name]
         self.logger.info("Dumping data to %s" % writer.fname)
-        if __has_pycuda__:
+        if __has_pycuda__:  # noqa: SIM102
             if isinstance(data, garray.GPUArray):
                 data = data.get()
 

nabu/pipeline/estimators.py

@@ -298,7 +298,7 @@ class SinoCORFinder(CORFinderBase):
         """
         Initialize a SinoCORFinder object.
 
-        Other parameters
+        Other Parameters
         ----------------
         The following keys can be set in cor_options.
 
@@ -341,7 +341,7 @@ class SinoCORFinder(CORFinderBase):
                 self.angles = self.dataset_info.rotation_angles[::subsampling]
                 self.subsampling = subsampling
         else:  # Angular step
-            raise NotImplementedError()
+            raise NotImplementedError
 
     def _load_raw_sinogram(self):
         if self.slice_idx is None:
@@ -441,7 +441,7 @@ class CompositeCORFinder(CORFinderBase):
 
     search_methods = {
         "composite-coarse-to-fine": {
-            "class": CenterOfRotation,  # Hack. Not used. Everything is done in the find_cor() func.
+            "class": CenterOfRotation,  # Not used. Everything is done in the find_cor() func.
         }
     }
     _default_cor_options = {"low_pass": 0.4, "high_pass": 10, "side": "near", "near_pos": 0, "near_width": 40}
@@ -786,7 +786,7 @@ class CompositeCORFinder(CORFinderBase):
         elif self.norm_order == 1:
             return self.error_metric_l1(common_right, common_left, common_blurred_right, common_blurred_left)
         else:
-            assert False, "this cannot happen"
+            raise RuntimeError("this cannot happen")
 
     def error_metric_l2(self, common_right, common_left):
         common = common_right - common_left
@@ -818,10 +818,10 @@ def oversample(radio, ovs_s):
     # Pre-initialisation: The original data falls exactly on the following strided positions in the new data array.
     result[:: ovs_s[0], :: ovs_s[1]] = radio
 
-    for k in range(0, ovs_s[0]):
+    for k in range(ovs_s[0]):
         # interpolation coefficient for axis 0
         g = k / ovs_s[0]
-        for i in range(0, ovs_s[1]):
+        for i in range(ovs_s[1]):
             if i == 0 and k == 0:
                 # this case subset was already exactly matched from before the present double loop,
                 # in the pre-initialisation line.

nabu/pipeline/fullfield/chunked.py

@@ -18,7 +18,7 @@ from ...preproc.phase import PaganinPhaseRetrieval
 from ...preproc.ctf import CTFPhaseRetrieval, GeoPars
 from ...reconstruction.sinogram import SinoNormalization
 from ...reconstruction.filtering import SinoFilter
-from ...reconstruction.mlem import __have_corrct__, MLEMReconstructor
+from ...reconstruction.mlem import MLEMReconstructor
 from ...processing.rotation import Rotation
 from ...reconstruction.rings import MunchDeringer, SinoMeanDeringer, VoDeringer
 from ...processing.unsharp import UnsharpMask
@@ -99,7 +99,6 @@ class ChunkedPipeline:
 
         Notes
         ------
-
         Using `margin` results in a lesser number of reconstructed slices.
         More specifically, if `margin = (V, H)`, then there will be `delta_z - 2*V`
         reconstructed slices (if the sub-region is in the middle of the volume)
@@ -175,7 +174,7 @@ class ChunkedPipeline:
             Data volume sub-region, in the form ((start_a, end_a), (start_z, end_z), (start_x, end_x))
             where the data volume has a layout (angles, Z, X)
         """
-        n_angles = self.dataset_info.n_angles
+        # n_angles = self.dataset_info.n_angles
         n_x, n_z = self.dataset_info.radio_dims
         c_a, c_z, c_x = self.chunk_shape
         if sub_region is None:
@@ -190,7 +189,7 @@ class ChunkedPipeline:
             # check sub-region
             for i, start_end in enumerate(sub_region):
                 start, end = start_end
-                if start is not None and end is not None:
+                if start is not None and end is not None:  # noqa: SIM102
                     if end - start != self.chunk_shape[i]:
                         raise ValueError(
                             "Invalid (start, end)=(%d, %d) for sub-region (dimension %d): chunk shape is %s, but %d-%d=%d != %d"
@@ -635,7 +634,7 @@ class ChunkedPipeline:
         if options["method"] == "mlem" and options["implementation"] in (None, "corrct"):
             self.reconstruction = self.MLEMClass(  # pylint: disable=E1102
                 (self.radios_shape[1],) + self.sino_shape,
-                angles_rad=-options["angles"],  # WARNING: mind the sign...
+                angles_rad=options["angles"],
                 shifts_uv=self.dataset_info.translations,  # In config file, one line per proj, each line is (tu,tv). Corrct expects one col per proj and (tv,tu).
                 cor=options["rotation_axis_position"],
                 n_iterations=options["iterations"],

nabu/pipeline/fullfield/dataset_validator.py

@@ -1,4 +1,3 @@
-import os
 from ..dataset_validator import DatasetValidatorBase
 
 

nabu/pipeline/fullfield/nabu_config.py

@@ -1,4 +1,5 @@
-from ..config_validators import *
+# ruff: noqa: F405
+from ..config_validators import *  # noqa: F403
 
 nabu_config = {
     "dataset": {

nabu/pipeline/fullfield/reconstruction.py

@@ -7,7 +7,7 @@ from silx.io import get_data
 from silx.io.url import DataUrl
 from tomoscan.esrf.volume.singleframebase import VolumeSingleFrameBase
 from ... import version as nabu_version
-from ...utils import check_supported, subdivide_into_overlapping_segment
+from ...utils import check_supported, first_generator_item, subdivide_into_overlapping_segment
 from ...resources.logger import LoggerOrPrint
 from ...resources.utils import is_hdf5_extension
 from ...io.writer import merge_hdf5_files, NXProcessWriter
@@ -61,7 +61,7 @@ class FullFieldReconstructor:
             Dictionary with cuda options passed to `nabu.cuda.processing.CudaProcessing`
 
 
-        Other parameters
+        Other Parameters
         -----------------
         Advanced options can be passed in the 'extra_options' dictionary. These can be:
 
@@ -132,7 +132,7 @@ class FullFieldReconstructor:
         if len(avail_gpus) == 0:
             return
         # pick first GPU by default. TODO: handle user's nabu_config["resources"]["gpu_id"]
-        self.resources["gpu_id"] = self._gpu_id = list(avail_gpus.keys())[0]
+        self.resources["gpu_id"] = self._gpu_id = first_generator_item(avail_gpus.keys())
 
     def _get_backend(self, backend, cuda_options):
         self._pipeline_cls = ChunkedPipeline
@@ -355,8 +355,8 @@ class FullFieldReconstructor:
         d2 = rec_cfg["sample_detector_dist"]
         n_z, _ = self.process_config.radio_shape(binning=True)
 
-        delta_z = self.process_config.rec_delta_z  # accounts_for_binning
-        overlap = ceil(delta_z * d2 / (d1 + d2))  # sqrt(2) missing ?
+        # delta_z = self.process_config.rec_delta_z  # accounts_for_binning
+        # overlap = ceil(delta_z * d2 / (d1 + d2))  # sqrt(2) missing ?
 
         max_overlap = ceil(n_z * d2 / (d1 + d2))  # sqrt(2) missing ?
 
@@ -685,7 +685,7 @@ class FullFieldReconstructor:
         # Prevent issue when out_dir is empty, which happens only if dataset/location is a relative path.
         # TODO this should be prevented earlier
         if out_dir is None or len(out_dir.strip()) == 0:
-            out_dir = dirname(dirname(self.results[list(self.results.keys())[0]]))
+            out_dir = dirname(dirname(self.results[first_generator_item(self.results.keys())]))
         #
         if output_file is None:
             output_file = join(out_dir, prefix + out_cfg["file_prefix"]) + ".hdf5"
@@ -766,7 +766,8 @@ class FullFieldReconstructor:
         out_cfg = self.process_config.nabu_config["output"]
         if output_file is None:
             output_file = (
-                join(dirname(list(self._histograms.values())[0]), out_cfg["file_prefix"] + "_histogram") + ".hdf5"
+                join(dirname(first_generator_item(self._histograms.values())), out_cfg["file_prefix"] + "_histogram")
+                + ".hdf5"
             )
         local_files = self.get_relative_files(files=list(self._histograms.values()))
         #
@@ -818,7 +819,7 @@ class FullFieldReconstructor:
     def merge_data_dumps(self, axis=1):
         # Collect in a dict where keys are step names (instead of task keys)
         dumps = {}
-        for task_key, data_dumps in self._data_dumps.items():
+        for task_key, data_dumps in self._data_dumps.items():  # noqa: PERF102
             for step_name, fname in data_dumps.items():
                 fname = join(basename(dirname(fname)), basename(fname))
                 if step_name not in dumps:

nabu/pipeline/helical/dataset_validator.py

@@ -1,4 +1,4 @@
-from ..fullfield.dataset_validator import *
+from ..fullfield.dataset_validator import FullFieldDatasetValidator
 from ...utils import copy_dict_items
 
 
@@ -10,10 +10,9 @@ class HelicalDatasetValidator(FullFieldDatasetValidator):
 
     def _check_slice_indices(self):
         """Slice indices can be far beyond what fullfield pipeline accepts, no check here, but
-        Nabu expects that rec_region is initialised here"""
+        Nabu expects that rec_region is initialised here
+        """
 
         what = ["start_x", "end_x", "start_y", "end_y", "start_z", "end_z"]
 
         self.rec_region = copy_dict_items(self.rec_params, what)
-
-        return

nabu/pipeline/helical/fbp.py

@@ -1,6 +1,6 @@
-from ...reconstruction.fbp import *
+import numpy as np
+from ...reconstruction.fbp import Backprojector
 from .filtering import HelicalSinoFilter
-from ...utils import convert_index
 
 
 class BackprojectorHelical(Backprojector):
@@ -25,9 +25,9 @@ class BackprojectorHelical(Backprojector):
 
     def set_custom_angles_and_axis_corrections(self, angles_rad, x_per_proj):
         """To arbitrarily change angles
-        Parameters
-        ==========
 
+        Parameters
+        ----------
         angles_rad: array of floats
            one angle per each projection in radians
 

nabu/pipeline/helical/filtering.py

@@ -68,26 +68,26 @@ class HelicalSinoFilter(CudaSinoFilter):
             "padding",
             filename=get_cuda_srcfile("helical_padding.cu"),
             signature="PPfiiiii",
-            options=[str("-DMIRROR_EDGES")],
+            options=["-DMIRROR_EDGES"],
         )
         self._pad_mirror_constant_kernel = self.cuda.kernel(
             "padding",
             filename=get_cuda_srcfile("helical_padding.cu"),
             signature="PPfiiiiiff",
-            options=[str("-DMIRROR_CONSTANT")],
+            options=["-DMIRROR_CONSTANT"],
         )
 
         self._pad_mirror_edges_variable_rot_pos_kernel = self.cuda.kernel(
             "padding",
             filename=get_cuda_srcfile("helical_padding.cu"),
             signature="PPPiiiii",
-            options=[str("-DMIRROR_EDGES_VARIABLE_ROT_POS")],
+            options=["-DMIRROR_EDGES_VARIABLE_ROT_POS"],
         )
         self._pad_mirror_constant_variable_rot_pos_kernel = self.cuda.kernel(
             "padding",
             filename=get_cuda_srcfile("helical_padding.cu"),
             signature="PPPiiiiiff",
-            options=[str("-DMIRROR_CONSTANT_VARIABLE_ROT_POS")],
+            options=["-DMIRROR_CONSTANT_VARIABLE_ROT_POS"],
         )
 
         self.d_mirror_indexes = self.cuda.allocate_array(
@@ -179,6 +179,7 @@ class HelicalSinoFilter(CudaSinoFilter):
         """
         Perform the sinogram siltering.
         redefined here to use also mirror data
+
         Parameters
         ----------
         sino: numpy.ndarray or pycuda.gpuarray.GPUArray

nabu/pipeline/helical/gridded_accumulator.py

@@ -29,8 +29,7 @@ class GriddedAccumulator:
         This class creates, for a selected volume slab, a standard set of radios from an helical dataset.
 
         Parameters
-        ==========
-
+        ----------
         gridded_radios : 3D np.array
            this is the stack of new radios which will be resynthetised, by this class,
            for a selected slab.
@@ -97,7 +96,7 @@ class GriddedAccumulator:
         self.flats_srcurrent = flats_srcurrent
 
         self.flat_indexes = flat_indexes
-        self.flat_indexes_reverse_map = dict(
+        self.flat_indexes_reverse_map = dict(  # noqa: C404
             [(global_index, local_index) for (local_index, global_index) in enumerate(flat_indexes)]
         )
         self.flats = flats
@@ -121,7 +120,7 @@ class GriddedAccumulator:
         the accumulators are ready.
 
         Parameters
-        ==========
+        ----------
         subchunk_slice: an object of the python class "slice"
           this slice slices the angular domain which corresponds to the useful
           projections  which are useful for the chunk, and whose informations
@@ -278,7 +277,7 @@ class GriddedAccumulator:
                 i_diag_list = [(i0 - 1) // 2, (i0 - 1) // 2 + len(self.diagnostic_searched_angles_rad_clipped)]
                 for i_redundancy, i_diag in enumerate(i_diag_list):
                     # print("IRED ", i_redundancy)
-                    if i_redundancy:
+                    if i_redundancy:  # noqa: SIM102
                         # to avoid, in z_stages with >360 range for one single stage, to fill the second items which should instead be filled by another stage.
                         if abs(original_zpix_transl - self.diagnostic_zpix_transl[i_diag_list[0]]) < 2.0:
                             # print( " >>>>>> stesso z" , i_redundancy )
@@ -306,7 +305,7 @@ class GriddedAccumulator:
                         self.diagnostic_radios[i_diag] += data_token * factor
                         self.diagnostic_weights[i_diag] += weight * factor
                         break
-                    else:
+                    else:  # noqa: RET508
                         pass
 
     class _ReframingInfos:
@@ -483,8 +482,8 @@ def overlap_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
 
 def padding_logic(subr_start_z, subr_end_z, dtasrc_start_z, dtasrc_end_z):
     """.......... and the missing ranges which possibly could be obtained by extension padding"""
-    t_h = subr_end_z - subr_start_z
-    s_h = dtasrc_end_z - dtasrc_start_z
+    # t_h = subr_end_z - subr_start_z
+    # s_h = dtasrc_end_z - dtasrc_start_z
 
     if dtasrc_start_z <= subr_start_z:
         target_lower_padding = None
@@ -503,9 +502,9 @@ def get_reconstruction_space(span_info, min_scanwise_z, end_scanwise_z, phase_ma
     """Utility function, so far used only by the unit test, which, given the span_info object, creates the auxiliary collection arrays
     and initialises the  my_z_min, my_z_end variable keeping into account the scan direction
     and the min_scanwise_z, end_scanwise_z input arguments
-    Parameters
-    ==========
 
+    Parameters
+    ----------
     span_info: SpanStrategy
 
     min_scanwise_z: int

nabu/pipeline/helical/helical_chunked_regridded.py

@@ -1,3 +1,4 @@
+# ruff: noqa
 # pylint: skip-file
 
 from os import path

nabu/pipeline/helical/helical_reconstruction.py

@@ -3,6 +3,8 @@ from math import ceil
 from time import time
 import numpy as np
 import copy
+
+from nabu.utils import first_generator_item
 from ...resources.logger import LoggerOrPrint
 from ...io.writer import merge_hdf5_files
 from ...cuda.utils import collect_cuda_gpus
@@ -18,7 +20,7 @@ except:
 
 from .helical_chunked_regridded_cuda import CudaHelicalChunkedRegriddedPipeline
 
-from ..fullfield.reconstruction import collect_cuda_gpus, FullFieldReconstructor
+from ..fullfield.reconstruction import FullFieldReconstructor
 
 avail_gpus = collect_cuda_gpus() or {}
 
@@ -53,7 +55,8 @@ class HelicalReconstructorRegridded:
             Dictionary with advanced options. Please see 'Other parameters' below
         cuda_options: dict, optional
             Dictionary with cuda options passed to `nabu.cuda.processing.CudaProcessing`
-        Other parameters
+
+        Other Parameters
         -----------------
         Advanced options can be passed in the 'extra_options' dictionary. These can be:
 
@@ -242,9 +245,9 @@ class HelicalReconstructorRegridded:
             "reconstruction" in process_config.processing_steps
             and process_config.processing_options["reconstruction"]["enable_halftomo"]
         ):
-            radios_and_sinos = True
+            radios_and_sinos = True  # noqa: F841
 
-        max_dz = process_config.dataset_info.radio_dims[1]
+        # max_dz = process_config.dataset_info.radio_dims[1]
         chunk_size = chunk_step
         last_good_chunk_size = chunk_size
         while True:
@@ -431,7 +434,7 @@ class HelicalReconstructorRegridded:
         angles_deg = np.rad2deg(angles_rad)
 
         redundancy_angle_deg = self.process_config.nabu_config["reconstruction"]["redundancy_angle_deg"]
-        do_helical_half_tomo = self.process_config.nabu_config["reconstruction"]["helical_halftomo"]
+        # do_helical_half_tomo = self.process_config.nabu_config["reconstruction"]["helical_halftomo"]
 
         self.logger.info("Creating SpanStrategy object for helical ")
         t0 = time()
@@ -460,7 +463,7 @@ class HelicalReconstructorRegridded:
         self.logger.debug("Creating a new pipeline object")
         args = [self.process_config, task["sub_region"]]
 
-        dz = self._get_delta_z(task)
+        # dz = self._get_delta_z(task)
 
         pipeline = self._pipeline_cls(
             *args,
@@ -542,7 +545,7 @@ class HelicalReconstructorRegridded:
         # Prevent issue when out_dir is empty, which happens only if dataset/location is a relative path.
         # TODO this should be prevented earlier
         if out_dir is None or len(out_dir.strip()) == 0:
-            out_dir = dirname(dirname(self.results[list(self.results.keys())[0]]))
+            out_dir = dirname(dirname(self.results[first_generator_item(self.results.keys())]))
         #
         if output_file is None:
             output_file = join(out_dir, prefix + out_cfg["file_prefix"]) + ".hdf5"