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

nabu/stitching/utils/utils.py

@@ -1,4 +1,4 @@
-from distutils.version import StrictVersion
+from distutils.version import StrictVersion  # pylint: disable=E0401
 from typing import Optional, Union
 import logging
 import functools
@@ -9,7 +9,6 @@ from nxtomo.utils.transformation import build_matrix, DetYFlipTransformation
 from silx.utils.enum import Enum as _Enum
 from scipy.fft import rfftn as local_fftn
 from scipy.fft import irfftn as local_ifftn
-from ..overlap import OverlapStitchingStrategy, ImageStichOverlapKernel
 from ..alignment import AlignmentAxis1, AlignmentAxis2, PaddedRawData
 from ...misc import fourier_filters
 from ...estimation.alignment import AlignmentBase
@@ -75,7 +74,7 @@ def find_frame_relative_shifts(
     """
     :param overlap_axis: axis in [0, 1] on which the overlap exists. In image space. So 0 is aka y and 1 as x
     """
-    if not overlap_axis in (0, 1):
+    if overlap_axis not in (0, 1):
         raise ValueError(f"overlap_axis should be in (0, 1). Get {overlap_axis}")
     from nabu.stitching.config import (
         KEY_LOW_PASS_FILTER,
@@ -146,7 +145,7 @@ def find_frame_relative_shifts(
     }
 
     res_algo = {}
-    for shift_alg in set((x_cross_correlation_function, y_cross_correlation_function)):
+    for shift_alg in set((x_cross_correlation_function, y_cross_correlation_function)):  # noqa: C405
         if shift_alg not in shift_methods:
             raise ValueError(f"requested image alignment function not handled ({shift_alg})")
         try:
@@ -249,7 +248,7 @@ def find_volumes_relative_shifts(
 
     w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
     start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
-    end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_frame.shape[0], lower_frame.shape[0]))
+    end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, upper_frame.shape[0], lower_frame.shape[0])
 
     if start_overlap == 0:
         overlap_upper_frame = upper_frame[-end_overlap:]
@@ -385,12 +384,10 @@ def find_projections_relative_shifts(
             cor_options=cor_options,
         )
 
-        estimated_shifts = tuple(
-            [
-                estimated_shifts[0],
-                (lower_scan_pos - upper_scan_pos),
-            ]
-        )
+        estimated_shifts = [
+            estimated_shifts[0],
+            (lower_scan_pos - upper_scan_pos),
+        ]
         x_cross_correlation_function = ShiftAlgorithm.NONE
 
     # } else we will compute shift from the flat projections
@@ -464,7 +461,8 @@ def find_projections_relative_shifts(
     start_overlap = max(estimated_shifts[axis_proj_space] // 2 - w_window_size // 2, 0)
     end_overlap = min(
         estimated_shifts[axis_proj_space] // 2 + w_window_size // 2,
-        min(upper_proj.shape[axis_proj_space], lower_proj.shape[axis_proj_space]),
+        upper_proj.shape[axis_proj_space],
+        lower_proj.shape[axis_proj_space],
     )
     o_upper_sel = numpy.array(range(-end_overlap, -start_overlap))
     overlap_upper_frame = numpy.take_along_axis(

nabu/tests.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 import sys
 import os
 import pytest

nabu/testutils.py

@@ -41,7 +41,10 @@ def generate_tests_scenarios(configurations):
       - the key is the name of a parameter
       - the value is one value of this parameter
     """
-    scenarios = [{key: val for key, val in zip(configurations.keys(), p_)} for p_ in product(*configurations.values())]
+    scenarios = [
+        {key: val for key, val in zip(configurations.keys(), p_)}  # noqa: C416
+        for p_ in product(*configurations.values())
+    ]
     return scenarios
 
 
@@ -81,12 +84,34 @@ def get_big_data(filename):
 
 
 def uncompress_file(compressed_file_path, target_directory):
-    with tarfile.open(compressed_file_path) as f:
-        f.extractall(path=target_directory)
+    if not tarfile.is_tarfile(compressed_file_path):
+        raise ValueError(f"Invalid tar file: {compressed_file_path}")
+
+    def is_safe_member(member, target_directory):
+        """Ensure the member does not extract outside the target directory."""
+        if not isinstance(member, tarfile.TarInfo):
+            return False  # Reject any unexpected type
+
+        abs_target = os.path.abspath(target_directory)
+        member_path = os.path.abspath(os.path.join(target_directory, member.name))
+        return member_path.startswith(abs_target)
+
+    def get_valid_members(tar):
+        members = [m for m in tar.getmembers() if is_safe_member(m, target_directory)]
+        if not members:
+            raise ValueError("No valid files to extract or archive contains unsafe paths.")
+        for member in members:
+            if not is_safe_member(member, target_directory):
+                raise ValueError(f"Unsafe path detected: {member.name}")
+
+    with tarfile.open(compressed_file_path, "r") as tar:
+        tar.extractall(  # noqa: S202 - what can be done in addition of the above checks ?
+            path=target_directory, members=get_valid_members(tar)
+        )
 
 
 def get_file(fname):
-    downloaded_file = dataset_downloaded_path = utilstest.getfile(fname)
+    downloaded_file = utilstest.getfile(fname)
     if ".tar" in fname:
         uncompress_file(downloaded_file, os.path.dirname(downloaded_file))
         downloaded_file = downloaded_file.split(".tar")[0]
@@ -204,10 +229,7 @@ def generate_nx_dataset(out_fname, image_key, data_volume=None, rotation_angle=N
     nx_entry = nx_dict["entry"]
 
     def _get_field(dict_, path):
-        if path.startswith("/"):
-            path = path[1:]
-        if path.endswith("/"):
-            path = path[:-1]
+        path = path.strip("/")
         split_path = path.split("/")
         if len(split_path) == 1:
             return dict_[split_path[0]]

nabu/utils.py

@@ -1,7 +1,7 @@
 from fnmatch import fnmatch
 from functools import partial
 import os
-from functools import partial, lru_cache
+from functools import lru_cache
 from itertools import product
 import warnings
 from time import time
@@ -94,7 +94,7 @@ def indices_to_slices(indices):
     jumps = np.hstack([-1, jumps, len(indices) - 1])
     slices = []
     for i in range(len(jumps) - 1):
-        slices.append(slice(indices[jumps[i] + 1], indices[jumps[i + 1]] + 1))
+        slices.append(slice(indices[jumps[i] + 1], indices[jumps[i + 1]] + 1))  # noqa: PERF401
     return slices
 
 
@@ -183,7 +183,7 @@ def list_match_queries(available, queries):
     for a in available:
         for q in queries:
             if fnmatch(a, q):
-                matches.append(a)
+                matches.append(a)  # noqa: PERF401
     return matches
 
 
@@ -211,7 +211,7 @@ def _sizeof(Type):
     return np.dtype(Type).itemsize
 
 
-class _Default_format(dict):
+class _DefaultFormat(dict):
     """
     https://docs.python.org/3/library/stdtypes.html
     """
@@ -224,7 +224,7 @@ def safe_format(str_, **kwargs):
     """
     Alternative to str.format(), but does not throw a KeyError when fields are missing.
     """
-    return str_.format_map(_Default_format(**kwargs))
+    return str_.format_map(_DefaultFormat(**kwargs))
 
 
 def get_ftype(url):
@@ -296,7 +296,7 @@ def view_as_images_stack(img):
 
 
 def rescale_integers(items, new_tot):
-    """ "
+    """
     From a given sequence of integers, create a new sequence
     where the sum of all items must be equal to "new_tot".
     The relative contribution of each item to the new total is approximately kept.
@@ -329,6 +329,8 @@ def merged_shape(shapes, axis=0):
         return (shapes[0][0], n_img, shapes[0][2])
     elif axis == 2:
         return shapes[0][:2] + (n_img,)
+    else:
+        raise ValueError
 
 
 def is_device_backend(backend):
@@ -371,7 +373,7 @@ def generate_powers():
     powers = product(*valuations)
     res = []
     for pw in powers:
-        res.append(np.prod(list(map(lambda x: x[0] ** x[1], zip(primes, pw)))))
+        res.append(np.prod(list(map(lambda x: x[0] ** x[1], zip(primes, pw)))))  # noqa: PERF401
     return np.unique(res)
 
 
@@ -422,10 +424,14 @@ def partition_dict(dict_, n_partitions):
 
 
 def first_dict_item(dict_):
-    keys = sorted(list(dict_.keys()))
+    keys = sorted(dict_.keys())
     return dict_[keys[0]]
 
 
+def first_generator_item(gen):
+    return next(iter(gen))  # instead of list(gen)[0]
+
+
 def subsample_dict(dic, subsampling_factor):
     """
     Subsample a dict where keys are integers.
@@ -437,7 +443,7 @@ def subsample_dict(dic, subsampling_factor):
     return res
 
 
-def compare_dicts(dic1, dic2):
+def compare_dicts(dic1, dic2):  # noqa: PLR0911
     """
     Compare two dictionaries. Return None if and only iff the dictionaries are the same.
 
@@ -629,7 +635,7 @@ def get_num_threads(n=None):
         return min(n_avail, n)
 
 
-class DictToObj(object):
+class DictToObj:
     """utility class to transform a dictionary into an object with dictionary items as members.
     Example:
 
@@ -646,14 +652,17 @@ def remove_parenthesis_or_brackets(input_str):
     """
     clear string from left and or roght parenthesis / braquets
     """
-    if input_str.startswith("(") and input_str.endswith(")") or input_str.startswith("[") and input_str.endswith("]"):
+    if (input_str.startswith("(") and input_str.endswith(")")) or (
+        input_str.startswith("[") and input_str.endswith("]")
+    ):
         input_str = input_str[1:-1]
     return input_str
 
 
 def filter_str_def(elmt):
     """clean elemt if is a string defined from a text file.
-    Remove some character that could have be put on left or right and some empty spaces"""
+    Remove some character that could have be put on left or right and some empty spaces
+    """
     if elmt is None:
         return None
     assert isinstance(elmt, str)
@@ -676,7 +685,7 @@ def convert_str_to_tuple(input_str: str, none_if_empty: bool = False):
     if isinstance(input_str, tuple):
         return input_str
     if not isinstance(input_str, str):
-        raise TypeError("input_str should be a string not {}, {}".format(type(input_str), input_str))
+        raise TypeError(f"input_str should be a string not {type(input_str)}, {input_str}")
     input_str = input_str.lstrip(" ").lstrip("(").lstrip("[").lstrip(" ").rstrip(" ")
     input_str = remove_parenthesis_or_brackets(input_str)
     input_str = input_str.replace("\n", ",")
@@ -767,7 +776,7 @@ def median2(img):
     Roughly same speed as scipy median filter, but more memory demanding.
     """
     img2 = extend_image_onepixel(img)
-    I = np.array(
+    img3 = np.array(
         [
             img2[0:-2, 0:-2],
             img2[0:-2, 1:-1],
@@ -780,7 +789,7 @@ def median2(img):
             img2[2:, 2:],
         ]
     )
-    return np.median(I, axis=0)
+    return np.median(img3, axis=0)
 
 
 # ------------------------------------------------------------------------------
@@ -820,6 +829,7 @@ def warning(msg):
                 print(msg)
                 res = func(*args, **kwargs)
                 return res
+            return None
 
         return wrapper
 
@@ -840,7 +850,7 @@ def deprecated(msg, do_print=False):
 
 def deprecated_class(msg, do_print=False):
     def decorator(cls):
-        class wrapper:
+        class Wrapper:
             def __init__(self, *args, **kwargs):
                 deprecation_warning(msg, do_print=do_print, func_name=cls.__name__)
                 self.wrapped = cls(*args, **kwargs)
@@ -849,7 +859,7 @@ def deprecated_class(msg, do_print=False):
             def __getattr__(self, name):
                 return getattr(self.wrapped, name)
 
-        return wrapper
+        return Wrapper
 
     return decorator
 
@@ -905,7 +915,7 @@ from warnings import catch_warnings
 # catch_warnings() does not have "action=XX" kwarg for python < 3.11
 from sys import version_info
 
-if version_info.major == 3 and version_info.minor < 11:
+if version_info.major == 3 and version_info.minor < 11:  # noqa: YTT204 - not sure about this
 
     def dummy(*args, **kwargs):
         pass

{nabu-2024.2.4.dist-info → nabu-2025.1.0.dev4.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nabu
-Version: 2024.2.4
+Version: 2025.1.0.dev4
 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>
@@ -49,35 +49,35 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy <2,>1.9.0
+Requires-Dist: numpy>1.9.0
 Requires-Dist: scipy
-Requires-Dist: h5py >=3.0
-Requires-Dist: silx >=0.15.0
-Requires-Dist: tomoscan >=2.1.0
+Requires-Dist: h5py>=3.0
+Requires-Dist: silx>=0.15.0
+Requires-Dist: tomoscan>=2.1.0
 Requires-Dist: psutil
 Requires-Dist: pytest
 Requires-Dist: tifffile
 Requires-Dist: tqdm
-Provides-Extra: doc
-Requires-Dist: sphinx ; extra == 'doc'
-Requires-Dist: cloud-sptheme ; extra == 'doc'
-Requires-Dist: myst-parser ; extra == 'doc'
-Requires-Dist: nbsphinx ; extra == 'doc'
 Provides-Extra: full
-Requires-Dist: scikit-image ; extra == 'full'
-Requires-Dist: PyWavelets ; extra == 'full'
-Requires-Dist: glymur ; extra == 'full'
-Requires-Dist: pycuda !=2024.1.1 ; extra == 'full'
-Requires-Dist: scikit-cuda ; extra == 'full'
-Requires-Dist: pycudwt ; extra == 'full'
-Requires-Dist: sluurp >=0.3 ; extra == 'full'
-Requires-Dist: pyvkfft ; extra == 'full'
-Provides-Extra: full_nocuda
-Requires-Dist: scikit-image ; extra == 'full_nocuda'
-Requires-Dist: PyWavelets ; extra == 'full_nocuda'
-Requires-Dist: glymur ; extra == 'full_nocuda'
-Requires-Dist: sluurp >=0.3 ; extra == 'full_nocuda'
-Requires-Dist: pyvkfft ; extra == 'full_nocuda'
+Requires-Dist: scikit-image; extra == "full"
+Requires-Dist: PyWavelets; extra == "full"
+Requires-Dist: glymur; extra == "full"
+Requires-Dist: pycuda!=2024.1.1; extra == "full"
+Requires-Dist: scikit-cuda; extra == "full"
+Requires-Dist: pycudwt; extra == "full"
+Requires-Dist: sluurp>=0.3; extra == "full"
+Requires-Dist: pyvkfft; extra == "full"
+Provides-Extra: full-nocuda
+Requires-Dist: scikit-image; extra == "full-nocuda"
+Requires-Dist: PyWavelets; extra == "full-nocuda"
+Requires-Dist: glymur; extra == "full-nocuda"
+Requires-Dist: sluurp>=0.3; extra == "full-nocuda"
+Requires-Dist: pyvkfft; extra == "full-nocuda"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cloud_sptheme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
 
 # Nabu