__init__.py

"""
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Welcome to the Hazen Command Line Interface
Usage:
    hazen <task> <folder> [--measured_slice_width=<mm>] [--report] [--calc_t1 | --calc_t2] [--plate_number=<n>] [--show_template_fit]
    [--show_relax_fits] [--show_rois] [--log=<lvl>] [--verbose]
    hazen -h|--help
    hazen -v|--version
Options:
    <task>    snr | slice_position | slice_width | spatial_resolution | uniformity | ghosting | relaxometry
    <folder>
    --report


"""
import logging
import os
import pprint
import importlib

import pydicom
from docopt import docopt
import numpy as np
from hazenlib.tools import is_dicom_file

__version__ = '0.5.1'

import hazenlib.exceptions

EXCLUDED_FILES = ['.DS_Store']


def rescale_to_byte(array):
    image_histogram, bins = np.histogram(array.flatten(), 255)
    cdf = image_histogram.cumsum()  # cumulative distribution function
    cdf = 255 * cdf / cdf[-1]  # normalize

    # use linear interpolation of cdf to find new pixel values
    image_equalized = np.interp(array.flatten(), bins[:-1], cdf)

    return image_equalized.reshape(array.shape).astype('uint8')


def is_enhanced_dicom(dcm: pydicom.Dataset) -> bool:
    """

    Parameters
    ----------
    dcm

    Returns
    -------
    bool

    Raises
    ------
    Exception
     Unrecognised SOPClassUID

    """

    if dcm.SOPClassUID == '1.2.840.10008.5.1.4.1.1.4.1':
        return True
    elif dcm.SOPClassUID == '1.2.840.10008.5.1.4.1.1.4':
        return False
    else:
        raise Exception('Unrecognised SOPClassUID')


def get_manufacturer(dcm: pydicom.Dataset) -> str:
    supported = ['ge', 'siemens', 'philips', 'toshiba', 'canon']
    manufacturer = dcm.Manufacturer.lower()
    for item in supported:
        if item in manufacturer:
            return item

    raise Exception(f'{manufacturer} not recognised manufacturer')


def get_average(dcm: pydicom.Dataset) -> float:
    if is_enhanced_dicom(dcm):
        averages = dcm.SharedFunctionalGroupsSequence[0].MRAveragesSequence[0].NumberOfAverages
    else:
        averages = dcm.NumberOfAverages

    return averages


def get_bandwidth(dcm: pydicom.Dataset) -> float:
    """
    Returns PixelBandwidth

    Parameters
    ----------
    dcm: pydicom.Dataset

    Returns
    -------
    bandwidth: float
    """
    bandwidth = dcm.PixelBandwidth
    return bandwidth


def get_num_of_frames(dcm: pydicom.Dataset) -> int:
    """
    Returns number of frames of dicom object

    Parameters
    ----------
    dcm: pydicom.Dataset
        DICOM object

    Returns
    -------

    """
    if len(dcm.pixel_array.shape) > 2:
        return dcm.pixel_array.shape[0]
    elif len(dcm.pixel_array.shape) == 2:
        return 1


def get_slice_thickness(dcm: pydicom.Dataset) -> float:
    if is_enhanced_dicom(dcm):
        try:
            slice_thickness = dcm.PerFrameFunctionalGroupsSequence[0].PixelMeasuresSequence[0].SliceThickness
        except AttributeError:
            slice_thickness = dcm.PerFrameFunctionalGroupsSequence[0].Private_2005_140f[0].SliceThickness
        except Exception:
            raise Exception('Unrecognised metadata Field for Slice Thickness')
    else:
        slice_thickness = dcm.SliceThickness

    return slice_thickness


def get_pixel_size(dcm: pydicom.Dataset) -> (float, float):
    manufacturer = get_manufacturer(dcm)
    try:
        if is_enhanced_dicom(dcm):
            dx, dy = dcm.PerFrameFunctionalGroupsSequence[0].PixelMeasuresSequence[0].PixelSpacing
        else:
            dx, dy = dcm.PixelSpacing
    except:
        print('Warning: Could not find PixelSpacing..')
        if 'ge' in manufacturer:
            fov = get_field_of_view(dcm)
            dx = fov / dcm.Columns
            dy = fov / dcm.Rows
        else:
            raise Exception('Manufacturer not recognised')

    return dx, dy


def get_TR(dcm: pydicom.Dataset) -> (float):
    """
    Returns Repetition Time (TR)

    Parameters
    ----------
    dcm: pydicom.Dataset

    Returns
    -------
    TR: float
    """

    try:
        TR = dcm.RepetitionTime
    except:
        print('Warning: Could not find Repetition Time. Using default value of 1000 ms')
        TR = 1000
    return TR


def get_rows(dcm: pydicom.Dataset) -> (float):
    """
    Returns number of image rows (rows)

    Parameters
    ----------
    dcm: pydicom.Dataset

    Returns
    -------
    rows: float
    """
    try:
        rows = dcm.Rows
    except:
        print('Warning: Could not find Number of matrix rows. Using default value of 256')
        rows = 256

    return rows


def get_columns(dcm: pydicom.Dataset) -> (float):
    """
    Returns number of image columns (columns)

    Parameters
    ----------
    dcm: pydicom.Dataset

    Returns
    -------
    columns: float
    """
    try:
        columns = dcm.Columns
    except:
        print('Warning: Could not find matrix size (columns). Using default value of 256.')
        columns = 256
    return columns


def get_field_of_view(dcm: pydicom.Dataset):
    # assumes square pixels
    manufacturer = get_manufacturer(dcm)

    if 'ge' in manufacturer:
        fov = dcm[0x19, 0x101e].value
    elif 'siemens' in manufacturer:
        fov = dcm.Columns * dcm.PixelSpacing[0]
    elif 'philips' in manufacturer:
        if is_enhanced_dicom(dcm):
            fov = dcm.Columns * dcm.PerFrameFunctionalGroupsSequence[0].PixelMeasuresSequence[0].PixelSpacing[0]
        else:
            fov = dcm.Columns * dcm.PixelSpacing[0]
    elif 'toshiba' in manufacturer:
        fov = dcm.Columns * dcm.PixelSpacing[0]
    else:
        raise NotImplementedError('Manufacturer not ge,siemens, toshiba or philips so FOV cannot be calculated.')

    return fov


def main():
    arguments = docopt(__doc__, version=__version__)

    task = importlib.import_module(f"hazenlib.{arguments['<task>']}")
    folder = arguments['<folder>']
    files = [os.path.join(folder, x) for x in os.listdir(folder) if x not in EXCLUDED_FILES]
    dicom_objects = [pydicom.read_file(x, force=True) for x in files if is_dicom_file(x)]
    pp = pprint.PrettyPrinter(indent=4, depth=1, width=1)
    if arguments['--report']:
        report = True
    else:
        report = False

    log_levels = {
        "critical": logging.CRITICAL,
        "debug": logging.DEBUG,
        "info": logging.INFO,
        "warning": logging.WARNING,
        "error": logging.ERROR

    }

    if arguments['--log'] in log_levels.keys():
        level = log_levels[arguments['--log']]
        logging.getLogger().setLevel(level)
    else:
        # logging.basicConfig()
        logging.getLogger().setLevel(logging.INFO)

    if not arguments['<task>'] == 'snr' and arguments['--measured_slice_width']:
        raise Exception("the (--measured_slice_width) option can only be used with snr")
    elif arguments['<task>'] == 'snr' and arguments['--measured_slice_width']:
        measured_slice_width = float(arguments['--measured_slice_width'])
        return pp.pprint(task.main(dicom_objects, measured_slice_width, report_path=report))

    if arguments['<task>'] == 'relaxometry':
        # Relaxometry arguments
        relaxometry_cli_args = {'--calc_t1', '--calc_t2', '--plate_number',
                                '--show_template_fit', '--show_relax_fits',
                                '--show_rois', '--verbose'}

        # Pass arguments with dictionary, stripping initial double dash ('--')
        relaxometry_args = {}

        for key in relaxometry_cli_args:
            relaxometry_args[key[2:]] = arguments[key]

        return pp.pprint(task.main(dicom_objects, report_path=report,
                                   **relaxometry_args))

    return pp.pprint(task.main(dicom_objects, report_path=report))