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read_file

phyllotaxis_analysis.read_file Link

This module contains a class and some functions to read and extract data from a csv file. We suppose that the data for each plant is stored in a column.

read_csv_file Link

read_csv_file(filename)

Read and extract divergence angles from a tab-separated CSV file.

This function reads a CSV file where each plant's data is stored in a column, converts valid integer values to integers, and returns them as nested lists.

Parameters:

Name Type Description Default
filename str

Path to the CSV file to be read. The file must use tab characters as delimiters.

 required

Returns:

Type Description
list of list of int

A nested list where each sublist contains integer values extracted from the CSV file. Returns an empty list if the file is not found or contains non-integer values.

Raises:

Type Description
FileNotFoundError

If the specified file does not exist.
ValueError

If the file contains non-integer values that cannot be converted.
Source code in src/phyllotaxis_analysis/read_file.py 
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def read_csv_file(filename):
    """Read and extract divergence angles from a tab-separated CSV file.

    This function reads a CSV file where each plant's data is stored in a column,
    converts valid integer values to integers, and returns them as nested lists.

    Parameters
    ----------
    filename : str
        Path to the CSV file to be read. The file must use tab characters as delimiters.

    Returns
    -------
    list of list of int
        A nested list where each sublist contains integer values extracted from the CSV file.
        Returns an empty list if the file is not found or contains non-integer values.

    Raises
    ------
    FileNotFoundError
        If the specified file does not exist.
    ValueError
        If the file contains non-integer values that cannot be converted.
    """
    try:
        with open(filename, 'r') as fobj:
            readerObj = csv.reader(fobj, delimiter='\t')
            mainList = [list(row) for row in readerObj]
            angles = []
            for row in mainList:
                current_row = []
                for angle in row:
                    if angle != "":
                        try:
                            current_row.append(int(angle))
                        except ValueError:
                            # Skip non-integer values or handle as needed
                            pass
                angles.append(current_row)
        return angles
    except FileNotFoundError:
        print(f"Error: File '{filename}' not found.")
        return []
    except Exception as e:
        print(f"Error reading file: {e}")
        return []

read_seq_file Link

read_seq_file(filename)

Read and extract data from a .seq file

Parameters: filename (str): file name to read

Returns: list: list of sequences of divergence angles

Raises: FileNotFoundError: If the file does not exist IOError: If there's an error reading the file

Source code in src/phyllotaxis_analysis/read_file.py 
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def read_seq_file(filename):
    """
    Read and extract data from a .seq file

    Parameters:
        filename (str): file name to read

    Returns:
        list: list of sequences of divergence angles

    Raises:
        FileNotFoundError: If the file does not exist
        IOError: If there's an error reading the file
    """
    anglesList = []
    seq = []

    try:
        with open(filename, 'r') as fobj:
            # Skip header (first 12 lines)
            for _ in range(12):
                next(fobj, None)

            # Process data lines
            for line in fobj:
                if len(line) > 3:
                    if '\\' in line[-4:]:
                        # Line continues in next line
                        splittedLine = line[:-3].split()
                        seq.extend([int(i) for i in splittedLine])
                    elif ')' in line[-4:]:
                        # End of sequence
                        splittedLine = line[:-8].split()
                        seq.extend([int(i) for i in splittedLine])
                        anglesList.append(seq)
                        seq = []

        return anglesList

    except (FileNotFoundError, IOError) as e:
        # Re-raise with more context
        raise type(e)(f"Error reading file {filename}: {str(e)}")

read_txt_data_file Link

read_txt_data_file(filename)

Reads a text data file containing angles represented by integer values and returns a list of lists with those values.

Parameters:

Name Type Description Default
filename str

The path to the text file that will be read, including its name and file extension (e.g., 'path/to/file.txt').

 required

Returns:

Name Type Description
angles_list list

A list of lists where each inner list contains three integer values representing angles in a line of the input text file. If there are any issues reading or parsing the file, an empty list will be returned.

Raises:

Type Description
FileNotFoundError

If the specified file does not exist.
ValueError

If the file contains non-integer values that cannot be converted.
Source code in src/phyllotaxis_analysis/read_file.py 
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def read_txt_data_file(filename):
    """Reads a text data file containing angles represented by integer values and returns
    a list of lists with those values.

    Parameters
    ----------
    filename : str
        The path to the text file that will be read, including its name and file
        extension (e.g., 'path/to/file.txt').

    Returns
    -------
    angles_list : list
        A list of lists where each inner list contains three integer values
        representing angles in a line of the input text file. If there are any issues
        reading or parsing the file, an empty list will be returned.

    Raises
    ------
    FileNotFoundError
        If the specified file does not exist.
    ValueError
        If the file contains non-integer values that cannot be converted.
    """
    anglesList = []
    try:
        with open(filename, 'r') as fobj:
            for line in fobj:
                # Strip whitespace from both ends instead of just removing last char
                line = line.strip()
                if not line:  # Skip empty lines
                    continue

                lineList = line.split(' ')
                try:
                    l = [int(i) for i in lineList if i]  # Skip empty strings
                    anglesList.append(l)
                except ValueError:
                    print(f"Warning: Skipping line with non-integer values: {line}")

        return anglesList
    except FileNotFoundError:
        print(f"Error: File '{filename}' not found")
        return []
    except Exception as e:
        print(f"Error reading file '{filename}': {e}")
        return []