comparison COBRAxy/flux_to_map.py @ 147:3fca9b568faf draft

Uploaded

146:88cf4543e210

import matplotlib.pyplot as plt

ERRORS = []
########################## argparse ##########################################
ARGS :argparse.Namespace
def process_args() -> argparse.Namespace:
    """
    Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code.

    Args:
        args : Always obtained (in file) from sys.argv

    
    parser.add_argument(
        '-colorm',  '--color_map',
        type = str,
        choices = ["jet", "viridis"])

    args :argparse.Namespace = parser.parse_args()
    args.net = True

    return args
          
############################ dataset input ####################################

        f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
        # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
        # all output files: I don't care, this was never the performance bottleneck of the tool and
        # there is no other net gain in saving and re-using the built string.
        ext,
        prefix = "result")

FIELD_NOT_AVAILABLE = '/'
def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
    fieldsAmt = len(fieldNames)
    with open(outPath.show(), "w", newline = "") as fd:

    min_flux_means = min(min_nonzero_abs(arr) for arr in means.values())

    medians = {key: median/max_flux_medians for key, median in medians.items()}
    means = {key: mean/max_flux_means for key, mean in means.items()}

    save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix="result"), colormap)
    save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix="result"), colormap)

    cmap = plt.get_cmap(colormap)

    for key in class_pat:
        # Create color mappings for median and mean

        key (str): The key identifying the specific map.

    Returns:
        None
    """
    svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix="result")
    utils.writeSvg(svgFilePath, metabMap)
    if ARGS.generate_pdf:
        pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix="result")
        pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix="result")
        convert_to_pdf(svgFilePath, pngPath, pdfPath)
    if not ARGS.generate_svg:
        os.remove(svgFilePath.show())



    
############################ MAIN #############################################
def main() -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.

    Returns:
        None

    Raises:
        sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
    """

    global ARGS
    ARGS = process_args()

    if os.path.isdir('result') == False: os.makedirs('result')
    
    core_map :ET.ElementTree = ARGS.choice_map.getMap(
        ARGS.tool_dir,
        utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
    # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.

147:3fca9b568faf

import matplotlib.pyplot as plt

ERRORS = []
########################## argparse ##########################################
ARGS :argparse.Namespace
def process_args(args:List[str] = None) -> argparse.Namespace:
    """
    Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code.

    Args:
        args : Always obtained (in file) from sys.argv

    
    parser.add_argument(
        '-colorm',  '--color_map',
        type = str,
        choices = ["jet", "viridis"])
    
    parser.add_argument(
        '-idop', '--output_path', 
        type = str,
        default='result',
        help = 'output path for maps')

    args :argparse.Namespace = parser.parse_args(args)
    args.net = True

    return args
          
############################ dataset input ####################################

        f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
        # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
        # all output files: I don't care, this was never the performance bottleneck of the tool and
        # there is no other net gain in saving and re-using the built string.
        ext,
        prefix = ARGS.output_path)

FIELD_NOT_AVAILABLE = '/'
def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
    fieldsAmt = len(fieldNames)
    with open(outPath.show(), "w", newline = "") as fd:

    min_flux_means = min(min_nonzero_abs(arr) for arr in means.values())

    medians = {key: median/max_flux_medians for key, median in medians.items()}
    means = {key: mean/max_flux_means for key, mean in means.items()}

    save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)
    save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)

    cmap = plt.get_cmap(colormap)

    for key in class_pat:
        # Create color mappings for median and mean

        key (str): The key identifying the specific map.

    Returns:
        None
    """
    svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix=ARGS.output_path)
    utils.writeSvg(svgFilePath, metabMap)
    if ARGS.generate_pdf:
        pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix=ARGS.output_path)
        pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix=ARGS.output_path)
        convert_to_pdf(svgFilePath, pngPath, pdfPath)
    if not ARGS.generate_svg:
        os.remove(svgFilePath.show())



    
############################ MAIN #############################################
def main(args:List[str] = None) -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.

    Returns:
        None

    Raises:
        sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
    """

    global ARGS
    ARGS = process_args(args)

    if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path)
    
    core_map :ET.ElementTree = ARGS.choice_map.getMap(
        ARGS.tool_dir,
        utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
    # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.