#!/usr/bin/env python
from __future__ import annotations

import logging
import os
import sys

import SimpleITK as sitk

import radiomics
from radiomics import featureextractor, getFeatureClasses


def tqdmProgressbar():
    """
    This function will setup the progress bar exposed by the 'tqdm' package.
    Progress reporting is only used in PyRadiomics for the calculation of GLCM and GLSZM in full python mode, therefore
    enable GLCM and full-python mode to show the progress bar functionality

    N.B. This function will only work if the 'click' package is installed (not included in the PyRadiomics requirements)
    """

    radiomics.setVerbosity(
        logging.INFO
    )  # Verbosity must be at least INFO to enable progress bar

    import tqdm

    radiomics.progressReporter = tqdm.tqdm


def clickProgressbar():
    """
    This function will setup the progress bar exposed by the 'click' package.
    Progress reporting is only used in PyRadiomics for the calculation of GLCM and GLSZM in full python mode, therefore
    enable GLCM and full-python mode to show the progress bar functionality.

    Because the signature used to instantiate a click progress bar is different from what PyRadiomics expects, we need to
    write a simple wrapper class to enable use of a click progress bar. In this case we only need to change the 'desc'
    keyword argument to a 'label' keyword argument.

    N.B. This function will only work if the 'click' package is installed (not included in the PyRadiomics requirements)
    """

    # Enable the GLCM class to show the progress bar
    extractor.enableFeatureClassByName("glcm")

    radiomics.setVerbosity(
        logging.INFO
    )  # Verbosity must be at least INFO to enable progress bar

    import click

    class progressWrapper:
        def __init__(self, iterable, desc=""):
            # For a click progressbar, the description must be provided in the 'label' keyword argument.
            self.bar = click.progressbar(iterable, label=desc)

        def __iter__(self):
            return (
                self.bar.__iter__()
            )  # Redirect to the __iter__ function of the click progressbar

        def __enter__(self):
            return (
                self.bar.__enter__()
            )  # Redirect to the __enter__ function of the click progressbar

        def __exit__(self, exc_type, exc_value, tb):
            return self.bar.__exit__(
                exc_type, exc_value, tb
            )  # Redirect to the __exit__ function of the click progressbar

    radiomics.progressReporter = progressWrapper


# Get some test data
testCase = "lung2"
# repositoryRoot points to the root of the repository. The following line gets that location if this script is run
# from it's default location in \pyradiomics\bin. Otherwise, it will point to some (invalid) folder, causing the
# getTestCase function to fail to find the test case in the repository. In that case, a test case will be downloaded to
# temporary files and it's location is returned.
repositoryRoot = os.path.abspath(os.path.join(os.getcwd(), ".."))
imageName, maskName = radiomics.getTestCase(testCase, repositoryRoot)

# Get the location of the example settings file
paramsFile = os.path.abspath(r"exampleSettings\exampleVoxel.yaml")

if (
    imageName is None or maskName is None
):  # Something went wrong, in this case PyRadiomics will also log an error
    print("Error getting testcase!")
    sys.exit()

# Regulate verbosity with radiomics.verbosity
# radiomics.setVerbosity(logging.INFO)

# Get the PyRadiomics logger (default log-level = INFO
logger = radiomics.logger
logger.setLevel(
    logging.DEBUG
)  # set level to DEBUG to include debug log messages in log file

# Write out all log entries to a file
handler = logging.FileHandler(filename="testLog.txt", mode="w")
formatter = logging.Formatter("%(levelname)s:%(name)s: %(message)s")
handler.setFormatter(formatter)
logger.addHandler(handler)

# Initialize feature extractor using the settings file
extractor = featureextractor.RadiomicsFeatureExtractor(paramsFile)
featureClasses = getFeatureClasses()

# Uncomment one of these functions to show how PyRadiomics can use the 'tqdm' or 'click' package to report progress when
# running in full python mode. Assumes the respective package is installed (not included in the requirements)

tqdmProgressbar()
# clickProgressbar()

print("Active features:")
for cls, orig_features in extractor.enabledFeatures.items():
    features = orig_features
    if features is None or len(features) == 0:
        features = [
            f
            for f, deprecated in featureClasses[cls].getFeatureNames().items()
            if not deprecated
        ]
    for f in features:
        print(f)
        print(getattr(featureClasses[cls], f"get{f}FeatureValue").__doc__)

print("Calculating features")
featureVector = extractor.execute(imageName, maskName, voxelBased=True)

for featureName, featureValue in featureVector.items():
    if isinstance(featureValue, sitk.Image):
        sitk.WriteImage(featureValue, f"{testCase}_{featureName}.nrrd")
        print(f'Computed {featureName}, stored as "{testCase}_{featureName}.nrrd"')
    else:
        print(f"{featureName}: {featureValue}")
