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src/libertem/io/dataset/hdf5.py

Summary

Maintainability
D
2 days
Test Coverage

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

        assert all(ts <= ps for (ts, ps) in zip(tileshape_nd, self.slice_nd.shape))
Severity: Info
Found in src/libertem/io/dataset/hdf5.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

        assert array_backend in (NUMPY, CUDA)
Severity: Info
Found in src/libertem/io/dataset/hdf5.py by bandit

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
Open

        assert len(tiling_scheme) == 1, "incompatible tiling scheme! (%r)" % (tiling_scheme)
Severity: Info
Found in src/libertem/io/dataset/hdf5.py by bandit

File hdf5.py has 729 lines of code (exceeds 400 allowed). Consider refactoring.
Open

import os
import contextlib
import typing
from typing import Optional
import warnings
Severity: Major
Found in src/libertem/io/dataset/hdf5.py - About 1 day to fix

    Cyclomatic complexity is too high in method get_partitions. (11)
    Open

        def get_partitions(self):
        # ds_shape = Shape(self.shape, sig_dims=self.sig_dims)
        ds_shape: Shape = self.meta['ds_raw_shape']
        ds_slice = Slice(origin=[0] * len(ds_shape), shape=ds_shape)
        target_size = self.target_size
    Severity: Minor
    Found in src/libertem/io/dataset/hdf5.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Function get_partitions has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

        def get_partitions(self):
        # ds_shape = Shape(self.shape, sig_dims=self.sig_dims)
        ds_shape: Shape = self.meta['ds_raw_shape']
        ds_slice = Slice(origin=[0] * len(ds_shape), shape=ds_shape)
        target_size = self.target_size
    Severity: Minor
    Found in src/libertem/io/dataset/hdf5.py - About 2 hrs to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Cyclomatic complexity is too high in method _do_initialize. (9)
    Open

        def _do_initialize(self):
        if self.ds_path is None:
            try:
                datasets = _get_datasets(self.path)
                largest_ds = max(datasets, key=lambda x: prod(x.shape))
    Severity: Minor
    Found in src/libertem/io/dataset/hdf5.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Cyclomatic complexity is too high in method _get_tiles_normal. (9)
    Open

        def _get_tiles_normal(self, tiling_scheme: TilingScheme, dest_dtype):
        with self._get_h5ds() as dataset:
            # because the dtype conversion done by HDF5 itself can be quite slow,
            # we need to use a buffer for reading in hdf5 native dtype:
            data_flat = np.zeros(tiling_scheme.shape, dtype=dataset.dtype).reshape((-1,))
    Severity: Minor
    Found in src/libertem/io/dataset/hdf5.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    H5DataSet has 21 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class H5DataSet(DataSet):
    """
    Read data from a HDF5 data set.

    Examples
    Severity: Minor
    Found in src/libertem/io/dataset/hdf5.py - About 2 hrs to fix

      Cyclomatic complexity is too high in method _get_subslices. (7)
      Open

          def _get_subslices(self, tiling_scheme):
        """
        Generate partition subslices for the given tiling scheme for the different cases.
        """
        if tiling_scheme.intent == "partition":
      Severity: Minor
      Found in src/libertem/io/dataset/hdf5.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in method adjust_tileshape. (6)
      Open

          def adjust_tileshape(self, tileshape, roi):
        chunks = self._chunks
        sig_shape = self.shape.sig
        if roi is not None:
            return (1,) + sig_shape
      Severity: Minor
      Found in src/libertem/io/dataset/hdf5.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Function _get_tiles_normal has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
      Open

          def _get_tiles_normal(self, tiling_scheme: TilingScheme, dest_dtype):
        with self._get_h5ds() as dataset:
            # because the dtype conversion done by HDF5 itself can be quite slow,
            # we need to use a buffer for reading in hdf5 native dtype:
            data_flat = np.zeros(tiling_scheme.shape, dtype=dataset.dtype).reshape((-1,))
      Severity: Minor
      Found in src/libertem/io/dataset/hdf5.py - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function _get_subslices has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def _get_subslices(self, tiling_scheme):
        """
        Generate partition subslices for the given tiling scheme for the different cases.
        """
        if tiling_scheme.intent == "partition":
      Severity: Minor
      Found in src/libertem/io/dataset/hdf5.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function _get_datasets has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

      def _get_datasets(path):
    datasets: list[HDF5ArrayDescriptor] = []

    try:
        timeout = int(os.environ.get('LIBERTEM_IO_HDF5_TIMEOUT_DEBUG', 3))
      Severity: Minor
      Found in src/libertem/io/dataset/hdf5.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function __init__ has 10 arguments (exceeds 8 allowed). Consider refactoring.
      Open

          def __init__(self, path, ds_path=None, tileshape=None, nav_shape=None, sig_shape=None,
      Severity: Major
      Found in src/libertem/io/dataset/hdf5.py - About 45 mins to fix

        Function _do_initialize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
        Open

            def _do_initialize(self):
        if self.ds_path is None:
            try:
                datasets = _get_datasets(self.path)
                largest_ds = max(datasets, key=lambda x: prod(x.shape))
        Severity: Minor
        Found in src/libertem/io/dataset/hdf5.py - About 35 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Function _get_subslices_chunked_tiled has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

            def _get_subslices_chunked_tiled(self, tiling_scheme, scheme_lookup, nav_dims, tileshape_nd):
        """
        general tiled reading w/ chunking outer loop is a chunk in
        signal dimensions, inner loop is over "rows in nav"
        """
        Severity: Minor
        Found in src/libertem/io/dataset/hdf5.py - About 25 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

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