Use of assert detected. The enclosed code will be removed when compiling to optimised byte code. Open
assert self._files_sorted is not None- Exclude checks
Use of assert detected. The enclosed code will be removed when compiling to optimised byte code. Open
assert self._sequence_start is not None- Exclude checks
Use of assert detected. The enclosed code will be removed when compiling to optimised byte code. Open
assert self.meta is not None- Exclude checks
Use of assert detected. The enclosed code will be removed when compiling to optimised byte code. Open
assert self.meta is not None and base_shape[-1] == self.meta.shape[-1]- Exclude checks
Use of assert detected. The enclosed code will be removed when compiling to optimised byte code. Open
assert self._files_sorted is not None- Exclude checks
File mib.py has 973 lines of code (exceeds 400 allowed). Consider refactoring. Open
import re
import os
from glob import glob, escape
import logging
from typing import TYPE_CHECKING, Generator, List, Optional, Sequence, Tuple, UnionCyclomatic complexity is too high in method read_header. (12) Open
def read_header(self) -> HeaderDict:
# FIXME: do this read via the IO backend!
with open(file=self.path, encoding="ascii", errors='ignore') as f:
header = f.read(1024)
filesize = os.fstat(f.fileno()).st_size- Read upRead up
- Exclude checks
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. |
Function decode_r1_swap_2x2 has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring. Open
def decode_r1_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
"""
RAW 1bit format: each pixel is actually saved as a single bit. 64 bits
need to be unpacked together. This is the quad variant.
- Read upRead up
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 _get_decode_r. (10) Open
def _get_decode_r(self):
bit_depth = self._bit_depth
layout = self._header['sensor_layout']
num_chips = self._header['num_chips']
if layout == (2, 2) and num_chips == 4:- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in method get_read_ranges. (10) Open
def get_read_ranges(
self, start_at_frame: int, stop_before_frame: int,
dtype, tiling_scheme: TilingScheme, sync_offset: int = 0,
roi: Union[np.ndarray, None] = None,
):- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in method __init__. (8) Open
def __init__(self, path, tileshape=None, scan_size=None, disable_glob=False,
nav_shape=None, sig_shape=None, sync_offset=0, io_backend=None):
super().__init__(io_backend=io_backend)
self._sig_dims = 2
self._path = path- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in function decode_r1_swap_2x2. (8) Open
@numba.njit(inline='always', cache=True, boundscheck=True)
def decode_r1_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
"""
RAW 1bit format: each pixel is actually saved as a single bit. 64 bits
need to be unpacked together. This is the quad variant.- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in function _mib_2x2_tile_block. (7) Open
@numba.njit(inline="always", cache=True)
def _mib_2x2_tile_block(
slices_arr, fileset_arr, slice_sig_sizes, sig_origins,
inner_indices_start, inner_indices_stop, frame_indices, sig_size,
px_to_bytes, bpp, frame_header_bytes, frame_footer_bytes, file_idxs,- Read upRead up
- Exclude checks
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. |
Function get_read_ranges has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring. Open
def get_read_ranges(
self, start_at_frame: int, stop_before_frame: int,
dtype, tiling_scheme: TilingScheme, sync_offset: int = 0,
roi: Union[np.ndarray, None] = None,
):- Read upRead up
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 _get_np_dtype. (6) Open
def _get_np_dtype(self, dtype: str, bit_depth: int) -> "nt.DTypeLike":
dtype = dtype.lower()
num_bits = int(dtype[1:])
if dtype[0] == "u":
num_bytes = num_bits // 8- Read upRead up
- Exclude checks
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. |
Cyclomatic complexity is too high in method _do_initialize. (6) Open
def _do_initialize(self):
self._headers = self._preread_headers()
self._files_sorted = list(sorted(self._files(),
key=lambda f: f.fields['sequence_first_image']))
- Read upRead up
- Exclude checks
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. |
Function read_header has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. Open
def read_header(self) -> HeaderDict:
# FIXME: do this read via the IO backend!
with open(file=self.path, encoding="ascii", errors='ignore') as f:
header = f.read(1024)
filesize = os.fstat(f.fileno()).st_size- Read upRead up
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 _mib_2x2_tile_block has 16 arguments (exceeds 8 allowed). Consider refactoring. Open
def _mib_2x2_tile_block(Function _get_decode_r has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def _get_decode_r(self):
bit_depth = self._bit_depth
layout = self._header['sensor_layout']
num_chips = self._header['num_chips']
if layout == (2, 2) and num_chips == 4:- Read upRead up
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 _mib_2x2_tile_block has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def _mib_2x2_tile_block(
slices_arr, fileset_arr, slice_sig_sizes, sig_origins,
inner_indices_start, inner_indices_stop, frame_indices, sig_size,
px_to_bytes, bpp, frame_header_bytes, frame_footer_bytes, file_idxs,
slice_offset, extra, sig_shape,- Read upRead up
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 encode_r1 has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def encode_r1(inp, out):
for y in range(out.shape[0]):
row_out = out[y]
row_in = inp[y]
for stripe in range(row_out.shape[0] // 8):- Read upRead up
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 _mib_r24_px_to_bytes has 10 arguments (exceeds 8 allowed). Consider refactoring. Open
def _mib_r24_px_to_bytes(Function _get_np_dtype has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def _get_np_dtype(self, dtype: str, bit_depth: int) -> "nt.DTypeLike":
dtype = dtype.lower()
num_bits = int(dtype[1:])
if dtype[0] == "u":
num_bytes = num_bits // 8- Read upRead up
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 9 arguments (exceeds 8 allowed). Consider refactoring. Open
def __init__(self, path, tileshape=None, scan_size=None, disable_glob=False,Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, path, tileshape=None, scan_size=None, disable_glob=False,
nav_shape=None, sig_shape=None, sync_offset=0, io_backend=None):
super().__init__(io_backend=io_backend)
self._sig_dims = 2
self._path = path- Read upRead up
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 decode_r1_swap has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def decode_r1_swap(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
"""
RAW 1bit format: each pixel is actually saved as a single bit. 64 bits
need to be unpacked together.
"""- Read upRead up
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 decode_r6_swap_2x2 has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def decode_r6_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
"""
RAW 6bit format: the pixels need to be re-ordered in groups of 8. `inp`
should have dtype uint8. This is the quad variant.
- Read upRead up
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 decode_r12_swap_2x2 has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def decode_r12_swap_2x2(inp, out, idx, native_dtype, rr, origin, shape, ds_shape):
"""
RAW 12bit format: the pixels need to be re-ordered in groups of 4. `inp`
should be an uint8 view on padded big endian 12bit data (">u2").
This is the quad variant.- Read upRead up
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"