# LiberTEM/LiberTEM

src/libertem/io/dataset/seq.py

### Summary

C
1 day

#### File `seq.py` has 558 lines of code (exceeds 400 allowed). Consider refactoring. Open

``````# Based on the SEQ reader of the PIMS project, with the following license:
#
#    Copyright (c) 2013-2014 PIMS contributors
#    https://github.com/soft-matter/pims
Found in src/libertem/io/dataset/seq.py - About 5 hrs to fix

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

``````    def __init__(self, path: str, scan_size: Tuple[int] = None, nav_shape: Tuple[int] = None,
sig_shape: Tuple[int] = None, sync_offset: int = 0, io_backend=None):
super().__init__(io_backend=io_backend)
self._path = path
# There might be '.seq.seq' and '.seq' in the wild``````

## 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 `xml_defect_coord_extractor` has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring. Open

``````def xml_defect_coord_extractor(bad_pixel_map, map_index, map_sizes):
"""
returns the chosen bad pixel map's defects

Parameters``````
Found in src/libertem/io/dataset/seq.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"

#### Cyclomatic complexity is too high in function xml_defect_coord_extractor. (7) Open

``````def xml_defect_coord_extractor(bad_pixel_map, map_index, map_sizes):
"""
returns the chosen bad pixel map's defects

Parameters``````

## 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 xml_generate_map_size. (7) Open

``````def xml_generate_map_size(exc_rows, exc_cols, exc_pix, size, metadata):
"""
This function will be responsible for generating new size based on the parameters.
returns an np array with the excluded pixels as True

``````

## 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 `xml_generate_map_size` has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open

``````def xml_generate_map_size(exc_rows, exc_cols, exc_pix, size, metadata):
"""
This function will be responsible for generating new size based on the parameters.
returns an np array with the excluded pixels as True

``````
Found in src/libertem/io/dataset/seq.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"

#### Function `__init__` has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open

``````    def __init__(self, path: str, scan_size: Tuple[int] = None, nav_shape: Tuple[int] = None,
sig_shape: Tuple[int] = None, sync_offset: int = 0, io_backend=None):
super().__init__(io_backend=io_backend)
self._path = path
# There might be '.seq.seq' and '.seq' in the wild``````
Found in src/libertem/io/dataset/seq.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"

#### Refactor this function to reduce its Cognitive Complexity from 16 to the 15 allowed. Open

``def xml_defect_coord_extractor(bad_pixel_map, map_index, map_sizes):``
Found in src/libertem/io/dataset/seq.py by sonar-python

Cognitive Complexity is a measure of how hard the control flow of a function is to understand. Functions with high Cognitive Complexity will be difficult to maintain.